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- PDB-4j9x: Crystal structure of the complex of a hydroxyproline epimerase (T... -

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Basic information

Entry
Database: PDB / ID: 4j9x
TitleCrystal structure of the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with trans-4-hydroxy-l-proline
ComponentsProline racemase family protein
KeywordsISOMERASE / EPIMERASE / 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
4-HYDROXYPROLINE / 4-hydroxyproline 2-epimerase
Similarity search - Component
Biological speciesPseudomonas protegens (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 the complex of a hydroxyproline epimerase (TARGET EFI-506499, PSEUDOMONAS FLUORESCENS PF-5) with trans-4-hydroxy-l-proline
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 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_asym_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_asym_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_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.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_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 family protein
B: Proline racemase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3896
Polymers72,0812
Non-polymers3084
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-26 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.755, 90.097, 103.913
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 family protein


Mass: 36040.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Strain: Pf-5 / Gene: PFL_1412 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4KGU2
#2: Chemical ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 5.6
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 20 mM TRANS-4-HYDROXY-L-PROLINE), Reservoir (0.17 M Ammonium Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 20 mM TRANS-4-HYDROXY-L-PROLINE), Reservoir (0.17 M Ammonium Acetate, 0.085 M Sodium Citrate pH 5.6, 25.5 %(w/v) PEG 4000, 15 %(v/v) Glycerol), Soak 2 minutes in (Reservoir + 20% Ethylene Glycol, 100 mM TRANS-4-HYDROXY-L-PROLINE), 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→103.913 Å / Num. all: 77405 / Num. obs: 77405 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7960.5311.566281110690.53199
1.79-1.96.30.3652.166068105360.36599.4
1.9-2.036.60.2393.265966100290.23999.8
2.03-2.196.90.1654.46372892930.16599.7
2.19-2.47.10.1245.66074286050.12499.8
2.4-2.697.20.16.55587778050.199.8
2.69-3.170.0767.44857269110.07699.6
3.1-3.870.0579.34142158900.05799.7
3.8-5.386.90.04711.73185446280.04799.6
5.38-90.0976.60.04511.91744326390.04598.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data 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: 1.7→32.763 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.7771 / SU ML: 0.15 / σ(F): 0 / σ(I): 0 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 3886 5.03 %RANDOM
Rwork0.1942 ---
all0.1958 77234 --
obs0.1958 77234 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 24.2369 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 20 630 5358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064828
X-RAY DIFFRACTIONf_angle_d1.0936552
X-RAY DIFFRACTIONf_chiral_restr0.082720
X-RAY DIFFRACTIONf_plane_restr0.006868
X-RAY DIFFRACTIONf_dihedral_angle_d13.5231730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72070.27541200.23552540266099
1.7207-1.74250.2911220.22052603272599
1.7425-1.76540.29571390.22922571271099
1.7654-1.78960.27841700.21622511268198
1.7896-1.81520.28011320.22082593272599
1.8152-1.84230.29191230.21362609273299
1.8423-1.87110.23771400.20922580272099
1.8711-1.90170.22841240.2022586271099
1.9017-1.93450.2211460.20226112757100
1.9345-1.96970.24031430.20612608275199
1.9697-2.00760.24331390.202226052744100
2.0076-2.04860.21971380.193725832721100
2.0486-2.09310.23331180.194826452763100
2.0931-2.14180.2261180.198426352753100
2.1418-2.19530.23331590.194825712730100
2.1953-2.25470.23021500.198326242774100
2.2547-2.3210.24991590.195225892748100
2.321-2.39590.23821320.197326252757100
2.3959-2.48150.22861460.204126242770100
2.4815-2.58080.27221400.200626112751100
2.5808-2.69820.22221420.203726332775100
2.6982-2.84040.25711320.2022644277699
2.8404-3.01820.23441410.198526402781100
3.0182-3.25110.21291480.18962660280899
3.2511-3.57790.20261360.183326542790100
3.5779-4.09480.20731310.178326822813100
4.0948-5.15570.17161400.16282722286299
5.1557-32.7630.19781580.19572789294798
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)
11.38130.38570.09390.7250.33880.41830.020.1492-0.1237-0.14270.01310.06990.0197-0.0904-0.21130.17570.004-0.11160.17730.00220.1299-30.1606-9.020510.9513
21.1481-0.38850.25431.2228-0.10010.7938-0.0310.0056-0.0147-0.0695-0.01010.13580.0389-0.06970.00270.1474-0.0171-0.08660.15310.02750.156-35.6348-11.574315.7699
30.9773-0.26990.03450.44150.2620.46520.0360.09730.1484-0.1981-0.02750.1064-0.0716-0.09940.00940.16530.0238-0.10.13370.0410.1356-34.0013.758613.0265
40.7822-0.16010.19821.1891-0.74441.0029-0.0917-0.3517-0.17280.56750.1243-0.00250.16780.1687-0.01820.35430.0776-0.04080.30440.03190.1768-38.52993.566442.6191
51.6602-0.00310.29150.4485-0.01390.6103-0.0642-0.22160.00210.21140.1165-0.0910.05510.0446-0.03620.24570.0286-0.08230.2125-0.0260.1555-30.89824.074237.3978
63.6895-0.1496-0.59671.369-0.0230.9559-0.2019-0.1514-0.18250.4270.24610.03260.18210.0809-0.36420.40130.0901-0.07460.24380.03980.1637-26.9426-4.43739.9644
70.9653-0.2183-0.17951.94630.06771.5602-0.2186-0.13730.24850.15970.1690.01730.05390.1408-0.00620.15640.0383-0.06580.1459-0.00950.1496-31.97354.100334.753
80.9656-0.69-0.35950.90820.5460.3456-0.029-0.0149-0.01810.10420.0585-0.00290.09050.0625-0.02150.15690.0297-0.06230.15620.02350.1517-31.55374.449929.7361
92.3604-2.233-0.31932.52540.35940.2968-0.03120.07960.30520.04350.1142-0.3833-0.0050.0269-0.0470.12220.0148-0.08030.1361-0.03460.1626-29.977115.387329.7825
101.6175-0.478-1.12381.20410.29771.3617-0.0610.0568-0.0629-0.1116-0.03040.0829-0.0938-0.11460.06240.12830.0385-0.06490.135-0.01010.2133-37.177114.537722.5766
110.67380.19070.03332.2291-0.23510.46810.0245-0.0133-0.1537-0.0179-0.0373-0.08280.0095-0.06710.01220.1437-0.0068-0.06390.1615-0.00270.1515-23.3996-16.735314.2134
121.55120.17040.1581.3711-0.10451.0020.01670.14740.011-0.230.0442-0.0993-0.04110.0464-0.05670.1623-0.001-0.0340.1157-0.0140.0847-7.2113-11.56310.9893
131.0029-0.06620.19991.7836-0.19370.7877-0.0316-0.00420.0262-0.0260.0526-0.33720.01630.1266-0.02330.123-0.0112-0.0480.1451-0.00920.1949-1.6815-10.826416.5291
140.6397-0.30760.12721.0989-0.3750.8152-0.045-0.039-0.03550.070.0339-0.1910.02170.0263-0.04820.1210.02-0.09590.1141-0.0360.2003-3.1182-25.954924.9712
152.64991.02250.39680.704-0.0882.1429-0.1699-0.2010.670.30790.11220.0837-0.452-0.21370.05430.38480.092-0.11320.1692-0.03780.2662-10.103-16.03340.2055
161.34640.41690.22360.6325-0.37780.9248-0.06790.09810.05750.31440.0806-0.3048-0.22290.17350.12720.24350.0103-0.14660.1759-0.04820.32290.8756-20.196735.4529
170.6317-0.95390.0321.5384-0.26230.4692-0.075-0.0315-0.06520.17710.09730.1112-0.0294-0.0791-0.03520.1370.0108-0.06610.12650.00370.1971-8.3461-30.083230.6906
181.6746-0.66930.5881.2549-0.2531.3597-0.040.11420.0704-0.0572-0.0397-0.1320.03750.2330.06350.15180.0101-0.08370.17760.00270.2718-0.1649-35.118722.6973
190.6363-0.0612-0.05081.0556-0.17790.29390.00160.04780.1118-0.0639-0.00330.0143-0.03760.07870.03790.1705-0.0173-0.06460.16350.01550.161-13.9831-3.82214.2151
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 71 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 136 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 159 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 175 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 176 through 195 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 225 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 226 through 249 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 250 through 267 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 268 through 287 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 288 through 310 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 30 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 31 through 88 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 89 through 175 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 176 through 196 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 197 through 213 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 214 through 267 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 268 through 287 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 288 through 310 )B0

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