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- PDB-1xvs: Crystal structure of apaG Protein from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 1xvs
TitleCrystal structure of apaG Protein from Vibrio cholerae
ComponentsProtein apaG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / apaG / MCSG APC26324 / Midwest Center for Structural Genomics / protein structure initiative / PSI
Function / homology
Function and homology information


error-free translesion synthesis
Similarity search - Function
Uncharacterised protein family ApaG / ApaG domain / ApaG domain / ApaG domain superfamily / ApaG domain / ApaG domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChang, C. / Joachimiak, A. / Li, H. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of apaG from Vibrio cholerae
Authors: Chang, C. / Joachimiak, A. / Li, H. / Moy, S. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 28, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein apaG
B: Protein apaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0413
Polymers28,9492
Non-polymers921
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.138, 67.998, 64.002
Angle α, β, γ (deg.)90.00, 131.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein Protein apaG


Mass: 14474.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: apaG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KUS3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Bis-Tris, Magnesium, Formate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 25, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 19199 / Num. obs: 18181 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.112
Reflection shellResolution: 2.01→2.1 Å / Redundancy: 5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5.6 / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1TZA

1tza


Resolution: 2.01→48 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.769 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26585 931 5.1 %RANDOM
Rwork0.17997 ---
all0.18426 17250 --
obs0.18426 17250 93.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.312 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å23.77 Å2
2---2.22 Å20 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.01→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1972 0 6 248 2226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0380.0222013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7491.9652731
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.365246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69725.10298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69815350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1971512
X-RAY DIFFRACTIONr_chiral_restr0.2120.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2840.2938
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.21369
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.791.51280
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55822018
X-RAY DIFFRACTIONr_scbond_it5.0933844
X-RAY DIFFRACTIONr_scangle_it7.3264.5713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 43 -
Rwork0.213 935 -
obs--69.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27410.2395-0.62091.2741-0.78711.46250.0164-0.03330.0473-0.11750.0284-0.12150.0958-0.0168-0.04470.07270.00450.0728-0.009-0.00420.026923.5770.8731.378
21.37231.0092-0.44411.3035-0.31430.144-0.01210.00180.1329-0.02480.02940.0470.04440.001-0.0173-0.0165-0.00810.00530.0195-0.00070.01282.7382.48924.88
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1241 - 124
2X-RAY DIFFRACTION2BB1 - 1241 - 124

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