[English] 日本語
Yorodumi
- PDB-5m4g: Crystal Structure of Wild-Type Human Prolidase with Mn ions -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m4g
TitleCrystal Structure of Wild-Type Human Prolidase with Mn ions
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / prolidase / peptidase / hydrolysis / pita-bread / metalloenzyme
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / amino acid metabolic process / negative regulation of programmed cell death / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / extracellular exosome
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / HYDROXIDE ION / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsWilk, P. / Weiss, M.S. / Mueller, U. / Dobbek, H.
CitationJournal: FEBS J. / Year: 2017
Title: Substrate specificity and reaction mechanism of human prolidase.
Authors: Wilk, P. / Uehlein, M. / Kalms, J. / Dobbek, H. / Mueller, U. / Weiss, M.S.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.5Jan 17, 2024Group: 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,20215
Polymers107,3042
Non-polymers89813
Water20,5551141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-68 kcal/mol
Surface area35230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.641, 108.282, 211.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1151-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND SEGID
211CHAIN B AND SEGID

NCS ensembles :
ID
1
2

-
Components

#1: Protein Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Peptidase D / Proline dipeptidase / Prolidase


Mass: 53651.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1141 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 10mM NaBorate, 690-760mM NaCitrate / PH range: 7.6-8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2015
RadiationMonochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.48→46.532 Å / Num. obs: 196786 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.41 % / Biso Wilson estimate: 17.49 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.51
Reflection shellResolution: 1.48→1.57 Å / Rmerge(I) obs: 1.074 / Mean I/σ(I) obs: 1.81 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OKN

2okn


Resolution: 1.48→43.18 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.4
RfactorNum. reflection% reflection
Rfree0.167 2100 1.07 %
Rwork0.151 --
obs0.151 196767 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.76 Å2
Refinement stepCycle: LAST / Resolution: 1.48→43.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 48 1141 8695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097864
X-RAY DIFFRACTIONf_angle_d1.24310663
X-RAY DIFFRACTIONf_dihedral_angle_d13.2872915
X-RAY DIFFRACTIONf_chiral_restr0.051162
X-RAY DIFFRACTIONf_plane_restr0.0071392
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A5377X-RAY DIFFRACTIONPOSITIONAL
12B5377X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4787-1.51310.32321360.295212580X-RAY DIFFRACTION98
1.5131-1.5510.26981390.260912929X-RAY DIFFRACTION100
1.551-1.59290.27181400.241312960X-RAY DIFFRACTION100
1.5929-1.63980.20631380.222312849X-RAY DIFFRACTION100
1.6398-1.69270.23811400.20512928X-RAY DIFFRACTION100
1.6927-1.75320.20671390.196112927X-RAY DIFFRACTION100
1.7532-1.82340.19861400.177412958X-RAY DIFFRACTION100
1.8234-1.90640.17021390.160812863X-RAY DIFFRACTION100
1.9064-2.00690.2141400.150413007X-RAY DIFFRACTION100
2.0069-2.13270.14951400.139912975X-RAY DIFFRACTION100
2.1327-2.29730.1531400.133812996X-RAY DIFFRACTION100
2.2973-2.52850.14361410.134913036X-RAY DIFFRACTION100
2.5285-2.89430.15641410.140213076X-RAY DIFFRACTION100
2.8943-3.64620.16791410.131313132X-RAY DIFFRACTION100
3.6462-43.20250.12991460.131813451X-RAY DIFFRACTION100
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)
10.395-0.06750.07750.4547-0.05180.26670.0317-0.03140.00280.15560.01460.0747-0.0609-0.0367-00.18360.02240.01910.16610.03040.123212.511319.648394.2117
20.4654-0.00440.2370.71810.04861.01170.0044-0.09460.04960.22970.01580.0476-0.2026-0.0178-0.00050.24250.01190.02890.17620.02890.13913.642221.019596.4107
30.17860.21970.00010.36270.05230.17760.0219-0.0143-0.0765-0.05140.0552-0.07470.00770.0813-00.15760.0374-0.01590.16640.00390.143118.622514.581565.3796
40.5845-0.0999-0.0370.83730.11980.8760.0430.0146-0.15030.00320.020.03450.12540.0427-0.00180.13160.0222-0.04210.12990.00460.145419.1927-3.725872.5262
50.95990.0260.20210.56380.00130.25590.00920.0063-0.0507-0.01930.0165-0.10240.00180.03710.00210.11850.02660.0010.12550.00390.11934.897629.998471.1473
60.06810.0237-0.05440.12440.00680.0883-0.1057-0.1053-0.02270.16990.0490.0253-0.0574-0.02880.00010.16850.0528-0.0090.20070.01750.19685.352138.079477.8521
70.9932-0.1555-0.1320.95690.12710.3456-0.0152-0.12340.22040.04220.0265-0.0011-0.09990.00260.00040.15050.0389-0.01380.14240.00070.149917.255653.518675.4076
81.08560.30960.27930.9155-0.21140.3889-0.00280.02790.107-0.0148-0.0170.1481-0.0683-0.1267-0.00070.18150.0405-0.01970.15710.0240.17328.876451.783270.385
90.0136-0.0011-0.0080.03590.01270.01150.00830.01320.0125-0.0031-0.0029-0.0257-0.01170.0161-0.00010.6145-0.2047-0.06240.6832-0.16940.59254.373847.764151.1637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 82 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 83 THROUGH 212 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 213 THROUGH 277 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 278 THROUGH 483 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 6 THROUGH 252 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 253 THROUGH 277 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 278 THROUGH 427 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 428 THROUGH 485 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 486 THROUGH 488 )

+
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://pdbjlvh1.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