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2a63

Solution structure of a stably monomeric mutant of lambda Cro produced by substitutions in the ball-and-socket interface

Method: SOLUTION NMR Dmax: 57.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulatory protein cro

Enterobacteria phage lambda

UniProt P03040

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 1–66 Mutation：A33W, F58D, Y26Q No other associated polymer SOLUTION NMR NMR measurement conditions：pH 5.3；293 K；Ionic strength (raw mmCIF value) no salt added；Pressure ambient NMR measurement conditions：pH 6.1；293 K；Ionic strength (raw mmCIF value) no salt added；Pressure ambient NMR measurement conditions：pH 6.1；298 K；Ionic strength (raw mmCIF value) no salt added；Pressure ambient NMR sample composition：2.5 mM lambda Cro A33W/F58D/Y26Q U-13C, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP | 90% H2O/10% D2O NMR sample composition：5 mM lambda Cro A33W/F58D/Y26Q U-15N, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP | 90% H2O/10% D2O NMR sample composition：5 mM lambda Cro A33W/F58D/Y26Q unlabelled, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP | 90% H2O/10% D2O NMR sample composition：5 mM lambda Cro A33W/F58D/Y26Q U-15N, 50mM Na-phosphate, 100% D2O, 0.01% sodium azide, 1 mM TSP | 100% D2O Resolution not provided

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 2A63 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1COP THREE-DIMENSIONAL DIMER STRUCTURE OF THE LAMBDA-CRO REPRESSOR IN SOLUTION AS DETERMINED BY HETERONUCLEAR MULTIDIMENSIONAL NMR Deposited 1995-06-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain D 1–66（66 aa）
Chain E 1–66（66 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1D1L CRYSTAL STRUCTURE OF CRO-F58W MUTANT Deposited 1999-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–61（61 aa） Fragment：LAMBDA CRO REPRESSOR
Mutation：F58W SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.2 M NH4SO4, 6% isopropanol, including a layer of Hampton's "Al's oil", pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Resolution 2.10 Å R-free 0.258
1D1L CRYSTAL STRUCTURE OF CRO-F58W MUTANT Deposited 1999-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–61（61 aa） Fragment：LAMBDA CRO REPRESSOR
Mutation：F58W SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.2 M NH4SO4, 6% isopropanol, including a layer of Hampton's "Al's oil", pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Resolution 2.10 Å R-free 0.258
1D1L CRYSTAL STRUCTURE OF CRO-F58W MUTANT Deposited 1999-09-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–61（61 aa） Fragment：LAMBDA CRO REPRESSOR
Mutation：F58W SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；2.2 M NH4SO4, 6% isopropanol, including a layer of Hampton's "Al's oil", pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Resolution 2.10 Å R-free 0.258
1D1M CRYSTAL STRUCTURE OF CRO K56-[DGEVK]-F58W MUTANT Deposited 1999-09-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–60（60 aa） Fragment：LAMBDA CRO REPRESSOR
Chain B 1–60（60 aa） Fragment：LAMBDA CRO REPRESSOR
Mutation：K56[DGEVK]-F58W Mutation：K56[DGEVK]-F58W No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；4.8 M SODIUM FORMATE, 0.5% BETA-OCTYLGLUCOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.05 Å R-free 0.298
1ORC CRO REPRESSOR INSERTION MUTANT K56-[DGEVK] Deposited 1995-10-30 Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–66（66 aa）
Mutation：INS(K56-DGEVK) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.54 Å
2ECS Lambda Cro mutant Q27P/A29S/K32Q at 1.4 A in space group C2 Deposited 2007-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–66（66 aa）
Chain B 1–66（66 aa）
Mutation：Q27P, A29S, K32Q Mutation：Q27P, A29S, K32Q SO4 SULFATE ION × 4 ACT ACETATE ION × 4 CL CHLORIDE ION × 1 LI LITHIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80% saturated lithium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.40 Å R-free 0.175
2ECS Lambda Cro mutant Q27P/A29S/K32Q at 1.4 A in space group C2 Deposited 2007-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–66（66 aa）
Chain B 1–66（66 aa）
Mutation：Q27P, A29S, K32Q Mutation：Q27P, A29S, K32Q SO4 SULFATE ION × 8 ACT ACETATE ION × 8 CL CHLORIDE ION × 2 LI LITHIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；80% saturated lithium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.40 Å R-free 0.175
2ORC CRO REPRESSOR INSERTION MUTANT K56-[DGEVK], NMR, 32 STRUCTURES Deposited 1998-01-20 Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–66（66 aa）
Mutation：INS(K56-DGEVK) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.6；298 K
Resolution not provided
2OVG Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 Deposited 2007-02-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–66（66 aa）
Mutation：Q27P, A29S, K32Q SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5 M lithium sulfate, 0.1 M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.35 Å R-free 0.171
2OVG Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 Deposited 2007-02-13 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–66（66 aa）
Mutation：Q27P, A29S, K32Q SO4 SULFATE ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5 M lithium sulfate, 0.1 M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.35 Å R-free 0.171
2OVG Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 Deposited 2007-02-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–66（66 aa）
Mutation：Q27P, A29S, K32Q SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.5 M lithium sulfate, 0.1 M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.35 Å R-free 0.171
3ORC CRYSTAL STRUCTURE OF AN ENGINEERED CRO MONOMER BOUND NONSPECIFICALLY TO DNA Deposited 1998-04-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 2–61（60 aa）
Mutation：INSERTION (K56-DGEVK) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；COCRYSTALS WERE OBTAINED BY MIXING A 1.5 MOLAR EXCESS OF THE 7BP DNA FRAGMENT WITH CRO K56-[DGEVK], COMBINING WITH AN EQUAL VOLUME OF PRECIPITANT BUFFER (140MM AMMONIUM ACETATE, 31% PEG 3350, 100MM ACETATE BUFFER PH 4.6), THEN EQUILIBRATING AGAINST THE PRECIPITANT BUFFER VIA THE HANGING-DROP METHOD AT ROOM TEMPERATURE., vapor diffusion - hanging drop, temperature 293K
Resolution 3.00 Å
4CRO PROTEIN-DNA CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURE OF A LAMBDA CRO-OPERATOR COMPLEX Deposited 1992-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–66（66 aa）
Chain B 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；NA CACODYLATE, NACL, pH 6.90, VAPOR DIFFUSION
Resolution 3.90 Å
4CRO PROTEIN-DNA CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURE OF A LAMBDA CRO-OPERATOR COMPLEX Deposited 1992-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain C 1–66（66 aa）
Chain D 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；NA CACODYLATE, NACL, pH 6.90, VAPOR DIFFUSION
Resolution 3.90 Å
4CRO PROTEIN-DNA CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURE OF A LAMBDA CRO-OPERATOR COMPLEX Deposited 1992-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain E 1–66（66 aa）
Chain F 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.9；NA CACODYLATE, NACL, pH 6.90, VAPOR DIFFUSION
Resolution 3.90 Å
5CRO REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA Deposited 1998-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–66（66 aa）
Chain O 1–66（66 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions microdialysis or batch；pH 7.5；CRYSTALS WERE OBTAINED IN THE PRESENCE OF ABOUT 1.2M PHOSPHATE BY MICRODIALYSIS OR BATCH TECHNIQUES., pH 7.5, microdialysis or batch
Resolution 2.30 Å
5CRO REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA Deposited 1998-04-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–66（66 aa）
Chain C 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions microdialysis or batch；pH 7.5；CRYSTALS WERE OBTAINED IN THE PRESENCE OF ABOUT 1.2M PHOSPHATE BY MICRODIALYSIS OR BATCH TECHNIQUES., pH 7.5, microdialysis or batch
Resolution 2.30 Å
5CRO REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA Deposited 1998-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric
Chain A 1–66（66 aa）
Chain B 1–66（66 aa）
Chain C 1–66（66 aa）
Chain O 1–66（66 aa）
Not recorded PO4 PHOSPHATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions microdialysis or batch；pH 7.5；CRYSTALS WERE OBTAINED IN THE PRESENCE OF ABOUT 1.2M PHOSPHATE BY MICRODIALYSIS OR BATCH TECHNIQUES., pH 7.5, microdialysis or batch
Resolution 2.30 Å
5CRO REFINED STRUCTURE OF CRO REPRESSOR PROTEIN FROM BACTERIOPHAGE LAMBDA Deposited 1998-04-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–66（66 aa）
Chain B 1–66（66 aa）
Chain C 1–66（66 aa）
Chain O 1–66（66 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions microdialysis or batch；pH 7.5；CRYSTALS WERE OBTAINED IN THE PRESENCE OF ABOUT 1.2M PHOSPHATE BY MICRODIALYSIS OR BATCH TECHNIQUES., pH 7.5, microdialysis or batch
Resolution 2.30 Å
6CRO CRYSTAL STRUCTURE OF LAMBDA-CRO BOUND TO A CONSENSUS OPERATOR AT 3.0 ANGSTROM RESOLUTION Deposited 1998-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: hexameric
Chain A 2–61（60 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；CRO PROTEIN WAS SUSPENDED IN 20MM SODIUM CACODYLATE PH6.9 THEN MIXED WITH A 30% EXCESS OF THE 19BP DNA FRAGMENT. THE COMPLEX WAS THEN MIXED WITH AN EQUAL VOLUME OF PRECIPITANT SOLUTION (70MM AMMONIUM SULFATE, 13% PEG3350) AND ALLOWED TO EQUILIBRATE VIA THE HANGING DROP METHOD AT ROOM TEMPERATURE. COCRYSTALS TYPICALLY TAKE 3-4 MONTHS TO APPEAR., vapor diffusion - hanging drop, temperature 293K
Resolution 3.00 Å

11 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RCRO_LAMBD
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–66； UniProt 1–66

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

SAXS profile for 2a63

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2a63
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2a63
Deposition date deposition_date2005-07-01
Structure title titleSolution structure of a stably monomeric mutant of lambda Cro produced by substitutions in the ball-and-socket interface
Keywords keywordshelix-turn-helix, monomer, ball-and-socket, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.52 Å
Radius of gyration Rg (electron density) rg_electron14.12 Å
Forward intensity I(0) i0313600000.00
Molecular weight molecular_weight148310.0 kDa
Excluded volume excluded_volume185990 ų
Envelope volume envelope_volume37251 ų
Hydration-shell volume shell_volume16096 ų
Envelope diameter envelope_diameter61.8 Å
Shell Rg shell_rg26.44 Å
Envelope Rg envelope_rg22.17 Å
Shape Rg shape_rg14.03 Å
Total Rg total_rg14.85 Å
Total atoms total_atoms21100
Residues n_residues1320
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.0 Å
Rg (real space) rg_real14.76 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real3.1360e+08
I(0) uncertainty (real space) i0_real_error4.1550e+06
Rg (reciprocal space) rg_reciprocal14.73 Å
I(0) (reciprocal space) i0_reciprocal313600000.0000
Solution quality estimate total_estimate0.6905
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.1 Å
Skewness Skewness skewness0.751
Kurtosis Kurtosis kurtosis0.392
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha127100.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.196; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.406; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2a63a_
Class classa — All alpha proteins
Fold Fold folda.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamilya.35.1 — lambda repressor-like DNA-binding domains
Family Family familya.35.1.2 — Phage repressors

CATH v4.4 (1 domains)

Domain ID domain_id2a63A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology240 — CRO Repressor
Homologous superfamily homologous superfamily10 — CRO Repressor
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8. Citations (1)

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9. Files and Curves (10)