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- PDB-1g31: GP31 CO-CHAPERONIN FROM BACTERIOPHAGE T4 -

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Basic information

Entry
Database: PDB / ID: 1g31
TitleGP31 CO-CHAPERONIN FROM BACTERIOPHAGE T4
ComponentsGP31
KeywordsCHAPERONE / CO-CHAPERONIN / GROES / IN VIVO PROTEIN FOLDING / BACTERIOPHAGE T4
Function / homology
Function and homology information


viral capsid assembly / protein folding chaperone / ATP binding
Similarity search - Function
Bacteriophage T4, Gp31, chaperonin-GroEL / 10 Kd Chaperonin, Protein Cpn10; Chain O / GroES chaperonin / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / Capsid assembly protein Gp31
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHunt, J.F. / Van Der Vies, S.M. / Henry, L. / Deisenhofer, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structural adaptations in the specialized bacteriophage T4 co-chaperonin Gp31 expand the size of the Anfinsen cage.
Authors: Hunt, J.F. / van der Vies, S.M. / Henry, L. / Deisenhofer, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Interplay of Structure and Disorder in Cochaperonin Mobile Loops
Authors: Landry, S.J. / Taher, A. / Georgopoulos, C. / Van Der Vies, S.M.
#2: Journal: Nature / Year: 1994
Title: Bacteriophage T4 Encodes a Co-Chaperonin that Can Substitute for Escherichia Coli Groes in Protein Folding
Authors: Van Der Vies, S.M. / Gatenby, A.A. / Georgopoulos, C.
#3: Journal: J.Mol.Biol. / Year: 1970
Title: A Factor Preventing the Major Head Protein of Bacteriophage T4 from Random Aggregation
Authors: Laemmli, U.K. / Beguin, F. / Gujer-Kellenberger, G.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP31
B: GP31
C: GP31
D: GP31
E: GP31
F: GP31
G: GP31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,87937
Polymers84,6447
Non-polymers2,23530
Water8,449469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-112 kcal/mol
Surface area42230 Å2
MethodPISA
2
A: GP31
B: GP31
C: GP31
D: GP31
E: GP31
F: GP31
G: GP31
hetero molecules

A: GP31
B: GP31
C: GP31
D: GP31
E: GP31
F: GP31
G: GP31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,75774
Polymers169,28814
Non-polymers4,46960
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area48940 Å2
ΔGint-459 kcal/mol
Surface area66590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.677, 157.677, 90.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11C-1151-

PO4

21C-1171-

PO4

31F-1181-

K

41G-1161-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.623075, -0.782161, -0.001407), (0.782047, 0.622952, 0.018243), (-0.013393, -0.012467, 0.999833)35.2338, -12.7517, 0.9521
2given(-0.225365, -0.974185, -0.013204), (0.973952, -0.225618, 0.022651), (-0.025045, -0.007756, 0.999656)67.1743, 7.0365, 1.2559
3given(-0.901124, -0.433383, -0.012472), (0.433264, -0.901198, 0.011123), (-0.016061, 0.00462, 0.99986)71.4279, 44.0966, 0.4075
4given(-0.900758, 0.434151, -0.01215), (-0.434304, -0.90062, 0.016235), (-0.003894, 0.019901, 0.999794)45.1188, 70.4855, -0.4154
5given(-0.22242, 0.974776, -0.018447), (-0.974942, -0.222296, 0.00854), (0.004224, 0.019884, 0.999793)8.2535, 66.6088, -0.5862
6given(0.628568, 0.777645, -0.013072), (-0.777635, 0.628677, 0.006972), (0.013639, 0.005783, 0.99989)-11.8673, 35.0277, -0.3685
7given(0.621384, -0.7835, 0.00301), (0.783396, 0.621357, 0.014339), (-0.013105, -0.006552, 0.999893)35.1386, -12.5778, 0.5485
8given(-0.225929, -0.974064, -0.012453), (0.97391, -0.226137, 0.019001), (-0.021324, -0.007835, 0.999742)67.161, 7.124, 1.079
9given(-0.899123, -0.437592, -0.00954), (0.437457, -0.899139, 0.01344), (-0.01446, 0.007911, 0.999864)71.2535, 43.7027, 0.1996
10given(-0.900446, 0.434845, -0.010317), (-0.434953, -0.900357, 0.013184), (-0.003556, 0.016359, 0.99986)44.9487, 70.5651, -0.4855
11given(-0.223508, 0.97454, -0.017786), (-0.974702, -0.223469, 0.004207), (0.000126, 0.018276, 0.999833)8.2645, 66.8969, -0.5453
12given(0.625108, 0.780498, -0.007966), (-0.780505, 0.625143, 0.002852), (0.007206, 0.004435, 0.999964)-12.1163, 35.2549, -0.3328

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Components

#1: Protein
GP31


Mass: 12091.999 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Cellular location: CYTOPLASM / Gene: 31 / Organ: BRAIN / Plasmid: PSV25 / Cellular location (production host): CYTOPLASM / Gene (production host): GROES / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009 / References: UniProt: P17313
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE PHOSPHATE AND POTASSIUM IONS WITH RESIDUE NUMBERS FROM 1151 - 1184 LIE IN 4 CO-PLANAR AND ...THE PHOSPHATE AND POTASSIUM IONS WITH RESIDUE NUMBERS FROM 1151 - 1184 LIE IN 4 CO-PLANAR AND CONCENTRIC RINGS WHICH ARE CHARACTERIZED BY A COINCIDENCE OF TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AND SEVEN-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY. THE TWO-FOLD CRYSTALLOGRAPHIC AXIS LIES IN THE PLANE OF THE RINGS, BISECTING THEM AND PASSING DIRECTLY THROUGH RESIDUES 1151, 1161, 1171, AND 1181 (WHICH THEREFORE LIE ON SPECIAL POSITIONS). RESIDUES 1151, 1161, AND 1171 ARE INORGANIC PHOSPHATE IONS (PO4) AND ONLY HALF OF THEIR COVALENT CHEMICAL STRUCTURE RESIDES IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, AND THE COMPLETE STRUCTURE IS PRODUCED BY APPLICATION OF THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY OPERATION. THE SEVEN-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY AXIS IS PERPENDICULAR TO THE CONCENTRIC RINGS OF INORGANIC IONS AND INTERSECTS THE TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS ESSENTIALLY AT THEIR CENTER. THEREFORE, APPLICATION OF TWO-FOLD CRYSTALLOGRAPHIC SYMMETRY TO RESIDUES 1151, 1152, 1153, AND 1154 PRODUCES A RING OF 7 INORGANIC PHOSPHATE IONS WHICH ARE RELATED BY NON-CRYSTALLOGRAPHIC SYMMETRY. SIMILARLY, RESIDUES 1161 - 1164 AND RESIDUES 1171 - 1174 GIVE RISE TO TWO ADDITIONAL RINGS OF INORGANIC PHOSPHATE IONS RELATED BY SEVEN-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY, WHILE RESIDUES 1181 THROUGH 1184 GIVE RISE TO A RING OF POTASSIUM IONS RELATED BY SEVEN-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY. IF THIS ALL MAKES YOUR BRAIN HURT (AS IT DID MINE), CHECK OUT FIGURE 1B IN THE PAPER ON THE CRYSTAL STRUCTURE OR LOOK DOWN THE SEVEN-FOLD AXIS OF THE GP31 OLIGOMER AFTER EXPANDING THE CONTENTS OF THE ASYMMETRIC UNIT BY CRYSTALLOGRAPHIC SYMMETRY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 65 %
Description: THE SEARCH MODEL CONTAINED ONLY 68% OF THE RESIDUES THAT EVENTUALLY APPEARED IN THE STRUCTURE AND THERE IS ONLY 17% SEQUENCE IDENTITY IN THIS REGION.
Crystal growDetails: PROTEIN WAS CRYSTALLIZED AT 17 MG/ML FROM 0.42 M NAH(2)PO(4), 1.70 M K(2)HPO(4), 10 MM BES, 6 MM DTT, 0.035% NAN(3), 29% ETHYLENE GLYCOL.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
24 mMdithiothreitol1drop
310 mMBES1drop
42 mMdithiothreitol1reservoir
50.42 Msodium phospahte1reservoir
61.70 Mpotassium phosphate1reservoir
729 %(v/v)ethylene glycol1reservoir
80.035 %(w/v)1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jan 1, 1997 / Details: BENT FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 42831 / % possible obs: 83.5 % / Observed criterion σ(I): 1 / Redundancy: 5.95 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.108 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.39 / % possible all: 65
Reflection
*PLUS
Rmerge(I) obs: 0.108

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ESCHERICHIA COLI GROES 2.8 ANGSTROM MODEL

Resolution: 2.3→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: THE CONFORMATION OF RESIDUES 25 - 31 IS VERY APPROXIMATELY DEFINED IN ALL 7 CHAINS BECAUSE OF THE DIFFUSE NATURE OF THE ELECTRON DENSITY IN THIS REGION. THE MOLECULAR IDENTITY OF 10.5 OF THE ...Details: THE CONFORMATION OF RESIDUES 25 - 31 IS VERY APPROXIMATELY DEFINED IN ALL 7 CHAINS BECAUSE OF THE DIFFUSE NATURE OF THE ELECTRON DENSITY IN THIS REGION. THE MOLECULAR IDENTITY OF 10.5 OF THE 17.5 PHOSPHATE IONS IN THE ASYMMETRIC UNIT WAS UNAMBIGUOUS BASED ON THEIR ELECTRON DENSITY IN AVERAGED MAPS AS WELL AS STEREOCHEMICAL AND REFINEMENT CRITERIA; THE MOLECULAR IDENTIFICATION OF THE OTHER SOLVENT IONS / MOLECULES REPRESENTS MORE TENTATIVE JUDGEMENTS BASED ON THE SAME CRITERIA.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4277 10 %SHELLS
Rwork0.225 ---
obs0.225 42831 83.5 %-
Displacement parametersBiso mean: 61.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å20 Å20 Å2
2---3.22 Å20 Å2
3---6.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5709 0 89 469 6267
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.751.5
X-RAY DIFFRACTIONx_mcangle_it7.132
X-RAY DIFFRACTIONx_scbond_it7.922
X-RAY DIFFRACTIONx_scangle_it11.742.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.50.03600
22X-RAY DIFFRACTION500.325
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.395 292 7 %
Rwork0.353 3853 -
obs--65.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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