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- PDB-2nrk: Crystal structure of conserved protein GrpB from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 2nrk
TitleCrystal structure of conserved protein GrpB from Enterococcus faecalis
ComponentsHypothetical protein GrpB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / UPF0157 / pfam04229 / glutamate-rich protein / Enterococcus faecalis / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyGrpB/Dephospho-CoA kinase / GrpB protein / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta / GrpB family protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsCuff, M.E. / Mulligan, R. / Bargassa, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of conserved protein GrpB from Enterococcus faecalis
Authors: Cuff, M.E. / Mulligan, R. / Bargassa, M. / Joachimiak, A.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE SURFACE CALCULATIONS INDICATE THAT THE BIOLOGICAL ASSEMBLY IS LIKELY TO BE A DIMER, BUT THIS HAS NOT BEEN EXPERIMENTALLY VERIFIED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein GrpB


Theoretical massNumber of molelcules
Total (without water)20,5131
Polymers20,5131
Non-polymers00
Water5,206289
1
A: Hypothetical protein GrpB

A: Hypothetical protein GrpB


Theoretical massNumber of molelcules
Total (without water)41,0262
Polymers41,0262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)73.665, 82.149, 30.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hypothetical protein GrpB


Mass: 20513.055 Da / Num. of mol.: 1 / Fragment: Targeted domain: Residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: UPF0157 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q837C3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2(6H2O), 0.1M HEPES pH 7.5, 22% Polyacrylic Acid 5100 Sodium salt, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97908, 0.97925
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 26, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979251
ReflectionResolution: 1.65→26.67 Å / Num. all: 21900 / Num. obs: 21900 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 31.62 Å2 / Rsym value: 0.052 / Net I/σ(I): 12.9
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.96 / Num. unique all: 1007 / Rsym value: 0.473 / % possible all: 65

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.65→26.67 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.659 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1115 5.1 %RANDOM
Rwork0.17769 ---
all0.17943 20784 --
obs0.17943 20784 94.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å20 Å2
2---1.13 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 289 1670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221470
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9551995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4924.8179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7615281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.867158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021127
X-RAY DIFFRACTIONr_nbd_refined0.2050.2737
X-RAY DIFFRACTIONr_nbtor_refined0.310.21019
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2238
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.226
X-RAY DIFFRACTIONr_mcbond_it0.8831.5878
X-RAY DIFFRACTIONr_mcangle_it1.49121384
X-RAY DIFFRACTIONr_scbond_it2.4873677
X-RAY DIFFRACTIONr_scangle_it4.0124.5604
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 69 -
Rwork0.248 1039 -
obs--66.59 %
Refinement TLS params.Method: refined / Origin x: 16.4474 Å / Origin y: 38.1567 Å / Origin z: 8.6054 Å
111213212223313233
T-0.0954 Å2-0.0129 Å2-0.0213 Å2--0.0743 Å2-0.0123 Å2---0.117 Å2
L1.2934 °2-0.6771 °20.0301 °2-1.5849 °2-0.166 °2--0.7571 °2
S0.026 Å °-0.05 Å °0.0125 Å °-0.031 Å °0.0429 Å °-0.011 Å °-0.0004 Å °0.135 Å °-0.0689 Å °

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