8qy2

Xylanase from Bacillus circulans mutant E78Q/F125A

Method: X-RAY DIFFRACTION D_max: 52.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endo-1,4-beta-xylanase

Niallia circulans subsp. circulans

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 29–213	Mutation：E78Q, F125A	GOL GLYCEROL × 3 ZN ZINC ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS pH 7.5	Resolution 1.70 Å R-free 0.214

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8QY2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BCX MUTATIONAL AND CRYSTALLOGRAPHIC ANALYSES OF THE ACTIVE SITE RESIDUES OF THE BACILLUS CIRCULANS XYLANASE Deposited 1994-04-01	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.81 Å
1BVV SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE Deposited 1998-09-18	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å
1C5H HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE Deposited 1999-11-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：CATALYTIC DOMAIN	Mutation：N35D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.55 Å
1C5I HYDROGEN BONDING AND CATALYSIS: AN UNEXPECTED EXPLANATION FOR HOW A SINGLE AMINO ACID SUBSTITUTION CAN CHANGE THE PH OPTIMUM OF A GLYCOSIDASE Deposited 1999-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：CATALYTIC DOMAIN	Mutation：N35D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.80 Å
1HV0 DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE Deposited 2001-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：Y80F_BCX	Mutation：Y80F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 1.60 Å
1HV1 DISSECTING ELECTROSTATIC INTERACTIONS AND THE PH-DEPENDENT ACTIVITY OF A FAMILY 11 GLYCOSIDASE Deposited 2001-01-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa） Fragment：Q127A_BCX	Mutation：Q127A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；ammonimu sulphate, sodium chloride, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298 K	Resolution 1.80 Å
1XNB HIGH-RESOLUTION STRUCTURES OF XYLANASES FROM B. CIRCULANS AND T. HARZIANUM IDENTIFY A NEW FOLDING PATTERN AND IMPLICATIONS FOR THE ATOMIC BASIS OF THE CATALYSIS Deposited 1994-06-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.49 Å
1XNC THERMOSTABILIZATION OF THE BACILLUS CIRCULANS XYLANASE, BY THE INTRODUCTION OF DISULFIDE BONDS Deposited 1994-06-01	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
2BVV SUGAR RING DISTORTION IN THE GLYCOSYL-ENZYME INTERMEDIATE OF A FAMILY G/11 XYLANASE. Deposited 1998-11-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：Y69F	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 1.50 Å
3LB9 Crystal structure of the B. circulans cpA123 circular permutant Deposited 2010-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–146（118 aa） Fragment：residues 65-182 and 2-63 Chain A 152–213（62 aa） Fragment：residues 65-182 and 2-63	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3LB9 Crystal structure of the B. circulans cpA123 circular permutant Deposited 2010-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–146（118 aa） Fragment：residues 65-182 and 2-63 Chain B 152–213（62 aa） Fragment：residues 65-182 and 2-63	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3LB9 Crystal structure of the B. circulans cpA123 circular permutant Deposited 2010-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 29–146（118 aa） Fragment：residues 65-182 and 2-63 Chain C 152–213（62 aa） Fragment：residues 65-182 and 2-63	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；298 K；13-20 % (NH4)2SO4 40 mM Tris-HCl, pH 8, VAPOR DIFFUSION, temperature 298K	Resolution 3.00 Å R-free 0.268
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E172H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZJ Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–213（185 aa）	Mutation：E172H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.41 Å R-free 0.343
3VZK Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.197
3VZK Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant Deposited 2012-10-14	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：N35E	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.55 Å R-free 0.197
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZL Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant Deposited 2012-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.266
3VZM Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E172H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.86 Å R-free 0.254
3VZN Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.67 Å R-free 0.236
3VZN Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：N35E	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.67 Å R-free 0.236
3VZO Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35H mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose Deposited 2012-10-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：N35H	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.73 Å R-free 0.200
7VUG Cryo-EM structure of a class A orphan GPCR in complex with Gi Deposited 2021-11-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7VUH Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
7VUI Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7VUJ Cryo-EM structure of a class A orphan GPCR Deposited 2021-11-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 29–213（185 aa）	Mutation：D39F, R150D, S62V	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 7ZQ 3-chloranyl-N-[2-oxidanylidene-2-[[(1S)-1-phenylethyl]amino]ethyl]benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7XN9 Crystal structure of SSTR2 and L-054,522 complex Deposited 2022-04-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GI9 tert-butyl (2S)-6-azanyl-2-[[(2R,3S)-3-(1H-indol-3-yl)-2-[[4-(2-oxidanylidene-3H-benzimidazol-1-yl)piperidin-1-yl]carbonylamino]butanoyl]amino]hexanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；100-400 mM lithium nitrate, 6-10% PEG2000, 100 mM L-054,522, and 0.1 M HEPES, pH 7.0	Resolution 2.60 Å R-free 0.265
7XNA Crystal structure of somatostatin receptor 2 (SSTR2) with peptide antagonist CYN 154806 Deposited 2022-04-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；293 K；100-300 mM ammonium sulphate, 6-10% PEG2000, 1 mg/ml CYN 154806, and 0.1 M HEPES, pH 7.0	Resolution 2.65 Å R-free 0.290
8QXY Xylanase from Bacillus circulans mutant E78Q bound to xylotriose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；5 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4	Resolution 1.41 Å R-free 0.211
8QXY Xylanase from Bacillus circulans mutant E78Q bound to xylotriose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；5 %v/v PEGSB, 0.071 M Zn Acet, 0.1 M BIS-TRIS, 0.2 M LiSO4	Resolution 1.41 Å R-free 0.211
8QXZ Xylanase from Bacillus circulans mutant E78Q/Y69A Deposited 2023-10-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 %v/v PEGSB, 0.2 M LiSO4, BIS-TRIS, pH 7.5	Resolution 1.50 Å R-free 0.183
8QXZ Xylanase from Bacillus circulans mutant E78Q/Y69A Deposited 2023-10-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 %v/v PEGSB, 0.2 M LiSO4, BIS-TRIS, pH 7.5	Resolution 1.50 Å R-free 0.183
8QY0 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylotriose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.197
8QY0 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylotriose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；25 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acet, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.197
8QY1 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylohexaose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.238
8QY1 Xylanase from Bacillus circulans mutant E78Q/Y69A bound to xylohexaose Deposited 2023-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, Y69A	ZN ZINC ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.1 M BIS-TRIS 7.5 pH	Resolution 1.90 Å R-free 0.238
8QY3 Xylanase from Bacillus circulans mutant E78Q/F125A bound to xylotriose Deposited 2023-10-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, F125A	ZN ZINC ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；22.5 %v/v PEGSB, 0.2 M LiSO4, 0.05 M Zn Acetate, 0.1 M BIS-TRIS, pH 7.5	Resolution 1.24 Å R-free 0.230
8R85 Xylanase from Bacillus circulans mutant E78Q/W9A Deposited 2023-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, W9A	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；18.182 %v/v PEGSH 0.1 M BICINE 9.16 pH	Resolution 1.30 Å R-free 0.172
8R86 Xylanase from Bacillus circulans mutant E78Q/W71A Deposited 2023-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–213（185 aa）	Mutation：E78Q, W71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.727 %v/v PEGSH, 0.1 M BICINE 8.81 pH	Resolution 1.50 Å R-free 0.173
8R86 Xylanase from Bacillus circulans mutant E78Q/W71A Deposited 2023-11-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 29–213（185 aa）	Mutation：E78Q, W71A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.727 %v/v PEGSH, 0.1 M BICINE 8.81 pH	Resolution 1.50 Å R-free 0.173
9M42 Structure-based discovery of potent agonists of the orphan receptor GPR139 Deposited 2025-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 27–213（187 aa）	Not recorded	A1L8O 2-[5-(4-methylthiophen-3-yl)-1,2,4-oxadiazol-3-yl]-~{N}-[(1~{S})-1-phenylethyl]ethanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9W0H S1P3 in complex with cpd-32 and spm242 Deposited 2025-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa） Fragment：H137Y, C84S, D39F, R150D	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.268
9W0L S1P3 in complex with CYM52581 and spm242 Deposited 2025-07-24	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 29–213（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.60 Å R-free 0.281

32 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	XYNA_NIACI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 29–213

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8qy2
Deposition date deposition_date	2023-10-25
Structure title title	Xylanase from Bacillus circulans mutant E78Q/F125A
Keywords keywords	HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.30 Å
Radius of gyration Rg (electron density) rg_electron	14.98 Å
Forward intensity I(0) i0	8818730.00
Molecular weight molecular_weight	20938.0 kDa
Excluded volume excluded_volume	25671 Å³
Envelope volume envelope_volume	27331 Å³
Hydration-shell volume shell_volume	15096 Å³
Envelope diameter envelope_diameter	51.4 Å
Shell Rg shell_rg	21.28 Å
Envelope Rg envelope_rg	15.17 Å
Shape Rg shape_rg	14.90 Å
Total Rg total_rg	16.21 Å
Total atoms total_atoms	1476
Residues n_residues	185
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	52.3 Å
Rg (real space) rg_real	16.14 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	8.8190e+06
I(0) uncertainty (real space) i0_real_error	8.9260e+04
Rg (reciprocal space) rg_reciprocal	16.16 Å
I(0) (reciprocal space) i0_reciprocal	8819000.0000
Solution quality estimate total_estimate	0.8024
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.1 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.474
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2867000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Endo-1,4-beta-xylanase
Molecular weight formula_weight	20331.9 kDa
Mutation mutation	E78Q, F125A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1618

ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIQYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTATQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW

来源 Source

来源生物 organism	Niallia circulans subsp. circulans
NCBI Class编号 ncbi_taxonomy_id	74308
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	209.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

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8. Citations (1)

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Unit-cell length a length_a	78.714 Å
Unit-cell length b length_b	78.714 Å
Unit-cell length c length_c	131.998 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	42.580 Å
R factor r_factor	0.1916
R_work r_work	0.1905
R_free r_free	0.2138

fit	/app/data/saxs_computation/qy/8qy2/8qy2.fit
pddf	/app/data/pr_computation/qy/8qy2/8qy2.pr.out
profile	/app/data/saxs_computation/qy/8qy2/8qy2.dat