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- PDB-4jci: Crystal structure of csal_2705, a putative hydroxyproline epimera... -

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Basic information

Entry
Database: PDB / ID: 4jci
TitleCrystal structure of csal_2705, a putative hydroxyproline epimerase from CHROMOHALOBACTER SALEXIGENS (TARGET EFI-506486), SPACE GROUP P212121, unliganded
ComponentsProline racemase
KeywordsISOMERASE / PUTATIVE HYDROXYPROLINE EPIMERASE / enzyme function initiative / EFI / Structural Genomics
Function / homology4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / 4-hydroxyproline 2-epimerase
Function and homology information
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of csal_2705, a putative hydroxyproline epimerase from CHROMOHALOBACTER SALEXIGENS (TARGET EFI-506486), space group P212121, unliganded
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, M. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionFeb 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline racemase
B: Proline racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6743
Polymers72,6512
Non-polymers231
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-27 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.095, 54.455, 253.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proline racemase / Epimerase


Mass: 36325.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / Gene: Csal_2705 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1QU06
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 298 K / pH: 4.8
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM PYRROLE-2-CARBOXYLATE), Reservoir (0.2 M di-Ammonium Citrate pH 5.0, 20 %(w/v) PEG 3350); Soak 2 minutes in (Reservoir + 20% ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM PYRROLE-2-CARBOXYLATE), Reservoir (0.2 M di-Ammonium Citrate pH 5.0, 20 %(w/v) PEG 3350); Soak 2 minutes in (Reservoir + 20% Glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→250 Å / Num. all: 72128 / Num. obs: 72128 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 19.43 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 17.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 3.3 / Num. unique all: 10077 / Rsym value: 0.644 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AZP

2azp


Resolution: 1.7→23.94 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8733 / SU ML: 0.18 / σ(F): 0 / σ(I): 0 / Phase error: 19.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3627 5.04 %RANDOM
Rwork0.1692 ---
all0.171 72011 --
obs0.171 72011 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.53 Å2 / Biso mean: 27.1603 Å2 / Biso min: 7.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4733 0 1 494 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114886
X-RAY DIFFRACTIONf_angle_d1.3326640
X-RAY DIFFRACTIONf_chiral_restr0.086713
X-RAY DIFFRACTIONf_plane_restr0.007880
X-RAY DIFFRACTIONf_dihedral_angle_d12.3441747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72240.26171330.23732536266995
1.7224-1.7460.28491270.23272443257093
1.746-1.77090.29791400.22182543268394
1.7709-1.79730.26421370.2152478261594
1.7973-1.82540.28151300.21352550268094
1.8254-1.85530.27731440.20762543268794
1.8553-1.88730.24431220.20422532265495
1.8873-1.92160.25151390.20462571271096
1.9216-1.95850.24411450.20062541268695
1.9585-1.99850.24631370.18882598273597
1.9985-2.04190.22121120.18352590270296
2.0419-2.08940.23021440.17532652279696
2.0894-2.14160.23171440.17562589273398
2.1416-2.19950.23711390.17482630276997
2.1995-2.26420.23631330.17552629276298
2.2642-2.33720.2011330.16772680281399
2.3372-2.42060.21061400.16722658279898
2.4206-2.51750.20161570.16952652280998
2.5175-2.63190.21651500.1672651280198
2.6319-2.77050.21151300.16172723285399
2.7705-2.94370.18921400.16772696283699
2.9437-3.17060.21141340.1572754288899
3.1706-3.48880.16071570.15532709286699
3.4888-3.99160.17741600.14132756291699
3.9916-5.02130.13891530.13142796294999
5.0213-23.940.21621470.19162884303197
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)
11.14510.4581-0.75520.51220.14021.25660.0122-0.0029-0.08250.05830.0276-0.11020.10610.211-0.03160.10840.0473-0.04140.1225-0.02840.145531.303339.693337.2278
20.4874-0.09320.07310.99940.33220.74660.05690.02170.0924-0.2659-0.11330.0651-0.1911-0.10030.02570.24560.0361-0.05090.081-0.00270.106519.30359.908349.3626
30.3556-0.0152-0.08090.49330.48551.30640.02080.02150.03050.0655-0.0449-0.0349-0.0836-0.04480.02190.10320.0104-0.02930.0539-0.00530.094919.88151.10547.774
40.85790.033-0.51480.521-0.29740.7449-0.05290.3283-0.073-0.0580.00480.00840.0478-0.26010.02370.1074-0.0264-0.01530.2475-0.05640.13378.338837.33417.753
50.8779-0.2078-0.2110.89230.10460.8702-0.01010.29190.2787-0.1705-0.0907-0.0334-0.2617-0.07540.07260.19310.0346-0.07240.31420.01250.26939.21360.40118.4735
61.0791-0.34010.07991.37710.46561.4176-0.00820.16740.1761-0.0553-0.09470.0861-0.1549-0.02270.09870.16350.0118-0.02360.19440.01780.212212.840261.88512.1455
70.83880.05060.17811.0217-0.1691.22510.00610.23260.042-0.1602-0.07980.02640.0557-0.10460.00930.07150.042-0.02790.1873-0.04130.122813.393844.529915.054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 118 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 195 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 196 through 309 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 114 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 115 through 175 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 176 through 267 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 268 through 308 )B0

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