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- PDB-4jbd: Crystal structure of Pput_1285, a putative hydroxyproline epimera... -

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Basic information

Entry
Database: PDB / ID: 4jbd
TitleCrystal structure of Pput_1285, a putative hydroxyproline epimerase from Pseudomonas putida f1 (target EFI-506500), open form, space group I2, bound citrate
ComponentsProline racemase
KeywordsISOMERASE / PUTATIVE HYDROXYPROLINE EPIMERASE / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity
Similarity search - Function
Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / 4-hydroxyproline 2-epimerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 pput_1285, a putative hydroxyproline epimerase from pseudomonas putida f1 (target efi-506500), open form, space group i2, bound citrate
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.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Other
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 / 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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5553
Polymers36,1711
Non-polymers3842
Water7,909439
1
A: Proline racemase
hetero molecules

A: Proline racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1106
Polymers72,3412
Non-polymers7684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3470 Å2
ΔGint-11 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.529, 54.166, 142.656
Angle α, β, γ (deg.)90.000, 96.570, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-702-

HOH

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Components

#1: Protein Proline racemase


Mass: 36170.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / ATCC 700007 / Gene: Pput_1285 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5VZY6
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / 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 Hydrogen Citrate, 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 Hydrogen Citrate, 20 %(w/v) PEG 3350). Soak 2 minutes in (Reservoir + 20% Glycerol), VAPOR DIFFUSION, SITTING DROP, 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: 1.3→70.859 Å / Num. all: 82749 / Num. obs: 82749 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 7.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4201 / Rsym value: 0.735 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AZP

2azp


Resolution: 1.3→22.118 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.8791 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4138 5 %RANDOM
Rwork0.158 ---
obs0.1593 82712 99.75 %-
all-82712 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.79 Å2 / Biso mean: 19.838 Å2 / Biso min: 8.56 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 26 439 2827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082477
X-RAY DIFFRACTIONf_angle_d1.2833375
X-RAY DIFFRACTIONf_chiral_restr0.073360
X-RAY DIFFRACTIONf_plane_restr0.007453
X-RAY DIFFRACTIONf_dihedral_angle_d14.619886
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31480.31141290.304526142743100
1.3148-1.33020.31521300.28442594272499
1.3302-1.34650.28081370.27542610274799
1.3465-1.36350.25791280.267425992727100
1.3635-1.38140.28071520.251225822734100
1.3814-1.40040.26061410.243526242765100
1.4004-1.42040.26431240.231925992723100
1.4204-1.44160.24921040.217226572761100
1.4416-1.46410.24831440.212626082752100
1.4641-1.48810.22331360.20226522788100
1.4881-1.51370.18731330.187225912724100
1.5137-1.54130.20631470.180826162763100
1.5413-1.57090.20611330.171126042737100
1.5709-1.60290.19641480.165726382786100
1.6029-1.63780.20441360.158726032739100
1.6378-1.67590.19161490.156326032752100
1.6759-1.71780.18151480.146526052753100
1.7178-1.76420.20361310.144525902721100
1.7642-1.81610.15121300.135826382768100
1.8161-1.87470.1451310.14426372768100
1.8747-1.94160.18121460.139426542800100
1.9416-2.01930.18721670.140725732740100
2.0193-2.11120.13771350.136826072742100
2.1112-2.22240.15231280.133726722800100
2.2224-2.36150.17871370.1326362773100
2.3615-2.54350.15451470.13626182765100
2.5435-2.79910.1561580.142826382796100
2.7991-3.2030.1741470.141126472794100
3.203-4.03150.14231150.139626722787100
4.0315-22.12150.21361470.1682593274096
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)
10.77770.10440.3430.5767-0.18180.50670.0487-0.134-0.00090.0197-0.04110.04790.0611-0.09060.02580.0729-0.01790.00470.1284-0.01180.0969-10.426920.122311.2527
20.0876-0.09830.02370.10670.00980.327-0.0537-0.003-0.0080.02640.0498-0.06670.038-0.02870.00530.1144-0.02280.00680.0961-0.00550.10042.708611.160924.0823
30.0910.08780.10590.5906-0.16250.289-0.05890.0979-0.0012-0.21420.0354-0.00420.1337-0.04720.00140.1638-0.01270.00510.12140.00090.12626.8376-3.555817.6839
4-0.016-0.11650.05910.2337-0.07660.2377-0.00730.001-0.0170.07090.00950.00580.0183-0.0288-0.00420.1014-0.0043-0.00110.09840.00580.10224.399511.688518.7455
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:88 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 89:159 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 160:225 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 226:308 )A0

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