3ezw

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices

Method: X-RAY DIFFRACTION D_max: 215.3 Å Quality: GOOD

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

Glycerol kinase

Escherichia coli

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–501 Chain B； UniProt 2–501 Chain E； UniProt 2–501 Chain G； UniProt 2–501	Mutation：G230D	GOL GLYCEROL × 4 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions：microfluidic free interface diffusion；pH 8.5；298 K；20% PEG 1500, 0.3 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL, pH 8.5, microfluidic free interface diffusion, temperature 298K	Resolution 2.00 Å R-free 0.225
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 2–501 Chain D； UniProt 2–501 Chain F； UniProt 2–501 Chain H； UniProt 2–501	Mutation：G230D	GOL GLYCEROL × 4 CL CHLORIDE ION × 4 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions：microfluidic free interface diffusion；pH 8.5；298 K；20% PEG 1500, 0.3 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL, pH 8.5, microfluidic free interface diffusion, temperature 298K	Resolution 2.00 Å R-free 0.225

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 3EZW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BO5 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 2–502（501 aa） Chain Z 2–502（501 aa）	Not recorded	FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS. 20 MM FBP WAS ADDED TO THE CRYO PROTECTION IN THE SOAKING EXPERIMENT	Resolution 3.20 Å
1BO5 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain O 2–502（501 aa） Chain Z 2–502（501 aa）	Not recorded	FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS. 20 MM FBP WAS ADDED TO THE CRYO PROTECTION IN THE SOAKING EXPERIMENT	Resolution 3.20 Å
1BO5 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-10	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 O 2–502（501 aa）	Not recorded	FBP 1,6-di-O-phosphono-beta-D-fructofuranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS. 20 MM FBP WAS ADDED TO THE CRYO PROTECTION IN THE SOAKING EXPERIMENT	Resolution 3.20 Å
1BO5 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Z 2–502（501 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN CRYSTALLIZED FROM LIQUOR CONTAINING 1 M SODIUM CITRATE, 0.1 M HEPES PH 7.5, 1 MM BME. CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS. 20 MM FBP WAS ADDED TO THE CRYO PROTECTION IN THE SOAKING EXPERIMENT	Resolution 3.20 Å
1BOT CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–501（501 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1M SODIUM CITRATE, 0.1M HEPES PH 7.5, 1MM BME, CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS	Resolution 3.05 Å
1BOT CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN ESCHERICHIA COLI GLYCEROL KINASE AND THE ALLOSTERIC REGULATOR FRUCTOSE 1,6-BISPHOSPHATE. Deposited 1998-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain Z 1–501（501 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；1M SODIUM CITRATE, 0.1M HEPES PH 7.5, 1MM BME, CRYO PROTECTION WAS ACHIEVED BY SOAKING CRYSTAL IN MOTHER LIQUOR CONTAINING 20% GLYCEROL FOR 4 HOURS	Resolution 3.05 Å
1BU6 CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION Deposited 1998-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain O 1–501（501 aa） Chain X 1–501（501 aa） Chain Y 1–501（501 aa） Chain Z 1–501（501 aa）	Mutation：A65T Mutation：A65T Mutation：A65T Mutation：A65T	SO4 SULFATE ION × 6 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；20-22% (W/V) POLYETHYLENE GLYCOL MR 4000 0.2 M LISO4 0.1 M TRIS PH 8.5 - 8.8 CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion - hanging drop	Resolution 2.37 Å
1BU6 CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION Deposited 1998-08-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–501（501 aa） Chain Y 1–501（501 aa）	Mutation：A65T Mutation：A65T	SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；20-22% (W/V) POLYETHYLENE GLYCOL MR 4000 0.2 M LISO4 0.1 M TRIS PH 8.5 - 8.8 CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion - hanging drop	Resolution 2.37 Å
1BU6 CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION Deposited 1998-08-30	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 X 1–501（501 aa） Chain Z 1–501（501 aa）	Mutation：A65T Mutation：A65T	SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；20-22% (W/V) POLYETHYLENE GLYCOL MR 4000 0.2 M LISO4 0.1 M TRIS PH 8.5 - 8.8 CRYSTALLIZED BY HANGING DROP VAPOR DIFFUSION AT ROOM TEMPERATURE., vapor diffusion - hanging drop	Resolution 2.37 Å
1BWF ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION Deposited 1998-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–501（501 aa） Chain Y 1–501（501 aa）	Mutation：S58W Mutation：S58W	MG MAGNESIUM ION × 2 ATF PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å
1GLA STRUCTURE OF THE REGULATORY COMPLEX OF ESCHERICHIA COLI IIIGLC WITH GLYCEROL KINASE Deposited 1992-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–501（501 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1GLB STRUCTURE OF THE REGULATORY COMPLEX OF ESCHERICHIA COLI IIIGLC WITH GLYCEROL KINASE Deposited 1992-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–501（501 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å
1GLC CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 4 MG MAGNESIUM ION × 4 G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å
1GLC CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 G3H GLYCERALDEHYDE-3-PHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å
1GLC CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 G3H GLYCERALDEHYDE-3-PHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.65 Å
1GLD CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–501（501 aa）	Not recorded	MN MANGANESE (II) ION × 4 G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.93 Å
1GLE CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 8 G3H GLYCERALDEHYDE-3-PHOSPHATE × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.94 Å
1GLE CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 4 G3H GLYCERALDEHYDE-3-PHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.94 Å
1GLE CATION PROMOTED ASSOCIATION (CPA) OF A REGULATORY AND TARGET PROTEIN IS CONTROLLED BY PHOSPHORYLATION Deposited 1994-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–501（501 aa）	Not recorded	ZN ZINC ION × 4 G3H GLYCERALDEHYDE-3-PHOSPHATE × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.94 Å
1GLF CRYSTAL STRUCTURES OF ESCHERICHIA COLI GLYCEROL KINASE AND THE MUTANT A65T IN AN INACTIVE TETRAMER: CONFORMATIONAL CHANGES AND IMPLICATIONS FOR ALLOSTERIC REGULATION Deposited 1998-08-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain O 2–502（501 aa） Chain X 2–502（501 aa） Chain Y 2–502（501 aa） Chain Z 2–502（501 aa）	Not recorded	PO4 PHOSPHATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.62 Å
1GLJ ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION Deposited 1998-09-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–501（501 aa） Chain Y 1–501（501 aa）	Mutation：S58W Mutation：S58W	MG MAGNESIUM ION × 1 ATS GAMMA-ARSONO-BETA, GAMMA-METHYLENEADENOSINE-5'-DIPHOSPHATE × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å
1GLL ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION Deposited 1998-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 1–501（501 aa） Chain Y 1–501（501 aa）	Mutation：S58W Mutation：S58W	MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 3.00 Å

12 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLPK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–500； UniProt 2–501 Author chain B； PDBConstruct 1–500； UniProt 2–501 Author chain C； PDBConstruct 1–500； UniProt 2–501 Author chain D； PDBConstruct 1–500； UniProt 2–501 Author chain E； PDBConstruct 1–500； UniProt 2–501 Author chain F； PDBConstruct 1–500； UniProt 2–501 Author chain G； PDBConstruct 1–500； UniProt 2–501 Author chain H； PDBConstruct 1–500； UniProt 2–501

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	3ezw
Deposition date deposition_date	2008-10-23
Structure title title	Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices
Keywords keywords	;GLYCEROL KINASE, GLYCEROL METABOLISM, ALLOSTERIC REGULATION, MICROFLUIDICS, IN SITU DATA COLLECTION, ATP-binding, Kinase, Metal-binding, Nucleotide-binding, Transferase ;; TRANSFERASE
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	70.77 Å
Radius of gyration Rg (electron density) rg_electron	71.45 Å
Forward intensity I(0) i0	2832490000.00
Molecular weight molecular_weight	444190.0 kDa
Excluded volume excluded_volume	553830 Å³
Envelope volume envelope_volume	774110 Å³
Hydration-shell volume shell_volume	97268 Å³
Envelope diameter envelope_diameter	237.3 Å
Shell Rg shell_rg	59.95 Å
Envelope Rg envelope_rg	70.37 Å
Shape Rg shape_rg	71.43 Å
Total Rg total_rg	71.30 Å
Total atoms total_atoms	31246
Residues n_residues	3939
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	215.3 Å
Rg (real space) rg_real	71.03 Å
Rg uncertainty (real space) rg_real_error	1.48 Å
I(0) (real space) i0_real	2.8270e+09
I(0) uncertainty (real space) i0_real_error	6.7580e+07
Rg (reciprocal space) rg_reciprocal	68.61 Å
I(0) (reciprocal space) i0_reciprocal	2818000000.0000
Solution quality estimate total_estimate	0.8104
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	58.7 Å
Skewness Skewness skewness	0.527
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.1100 Å⁻¹
Current regularization parameter α current_alpha	0.0121
Highest regularization parameter α highest_alpha	82040000.0000
Real-space data points n_real_points	23
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.057

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Glycerol kinase
Molecular weight formula_weight	59204.6 kDa
EC 编号 ec_number	2.7.1.30
Mutation mutation	G230D
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,G,C,D,F,H
Atom count atom_count	32916

TEKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIDGKGGTRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEHDQLYTRASQPELAPEDPEDLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

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	8

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	19

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1526

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7. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d3ezwa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwg1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwh1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

Domain ID domain_id	d3ezwh2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.4 — Glycerol kinase

CATH v4.4 (16 domains)

Domain ID domain_id	3ezwA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3ezwH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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8. Citations (1)

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Unit-cell length a length_a	91.116 Å
Unit-cell length b length_b	114.260 Å
Unit-cell length c length_c	212.624 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.15 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1679
R_work r_work	0.1667
R_free r_free	0.2248

fit	/app/data/saxs_computation/ez/3ezw/3ezw.fit
pddf	/app/data/pr_computation/ez/3ezw/3ezw.pr.out
profile	/app/data/saxs_computation/ez/3ezw/3ezw.dat