[English] 日本語
Yorodumi
- PDB-4j9x: Crystal structure of the complex of a hydroxyproline epimerase (T... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 630 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more