[English] 日本語
Yorodumi
- PDB-5cde: R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cde
TitleR372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris
ComponentsProline dipeptidase
KeywordsHYDROLASE / Xaa-Pro dipeptidase / Xanthomonas campestris / prolidase
Function / homology
Function and homology information


Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / 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 ...Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / 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
Biological speciesXanthomonas campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
CitationJournal: To Be Published
Title: R372A mutant of Xaa-Pro dipeptidase from Xanthomonas campestris at 1.85 Angstrom resolution
Authors: Kumar, A. / Are, V. / Ghosh, B. / Jamdar, S. / Makde, R.
History
DepositionJul 3, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,00712
Polymers85,2612
Non-polymers74610
Water9,602533
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-337 kcal/mol
Surface area28970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.088, 101.947, 111.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Proline dipeptidase


Mass: 42630.359 Da / Num. of mol.: 2 / Mutation: R372A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris (bacteria) / Strain: ATCC 33913 / NCPPB 528 / LMG 568 / Gene: pepQ, XCC2409 / Plasmid: pST50Tr / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8P839
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 5.5
Details: 0.1 M BisTris pH 5.5, 0.2 M Lithium sulphate, 25 % PEG 3350, 1 mM ZnCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1.28225 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2015 / Details: x-ray mirror
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28225 Å / Relative weight: 1
ReflectionResolution: 1.85→46.36 Å / Num. obs: 77891 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Net I/σ(I): 20.1 / Num. measured all: 539390 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.85-1.895.50.6862.11964735890.80.31979.8
9.43-46.365.90.0335440276810.9990.01497.7

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
PHENIX1.9_1692refinement
RESOLVEphasing
SOLVEphasing
Aimless0.5.7data scaling
XDSdata processing
RefinementMethod to determine structure: SAD / Resolution: 1.85→34.921 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 3877 4.99 %Random selection
Rwork0.1846 73804 --
obs0.1866 77681 97.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.99 Å2 / Biso mean: 32.2078 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 1.85→34.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5982 0 22 533 6537
Biso mean--39.61 36.07 -
Num. residues----795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076134
X-RAY DIFFRACTIONf_angle_d1.0978370
X-RAY DIFFRACTIONf_chiral_restr0.042934
X-RAY DIFFRACTIONf_plane_restr0.0051116
X-RAY DIFFRACTIONf_dihedral_angle_d13.0512184
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 (%)
1.85-1.87260.29491150.25952065218078
1.8726-1.89630.3361090.26292240234984
1.8963-1.92120.27171220.2492380250289
1.9212-1.94750.27581380.23692576271497
1.9475-1.97540.29321220.228326802802100
1.9754-2.00480.28951420.215726452787100
2.0048-2.03620.26151330.208326832816100
2.0362-2.06950.27671530.212526772830100
2.0695-2.10520.24141450.218326382783100
2.1052-2.14350.261270.210626822809100
2.1435-2.18470.29411400.205726582798100
2.1847-2.22930.26611560.200726602816100
2.2293-2.27780.23041540.192526512805100
2.2778-2.33080.21461330.192226632796100
2.3308-2.3890.26221370.19032669280699
2.389-2.45360.26071570.197926542811100
2.4536-2.52580.26991340.20242685281999
2.5258-2.60730.29691280.19592693282199
2.6073-2.70040.22521320.19852675280799
2.7004-2.80850.27291440.20952674281899
2.8085-2.93630.25151500.20272666281699
2.9363-3.0910.22811340.19812697283199
3.091-3.28450.24261580.188226932851100
3.2845-3.53790.20091270.17762720284799
3.5379-3.89350.15241680.151926882856100
3.8935-4.45590.17021450.143227492894100
4.4559-5.61020.17441300.149527802910100
5.6102-34.92720.21311440.17232863300798
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)
10.89190.46220.69622.27432.30164.0717-0.03490.11450.4932-0.5383-0.1590.0298-1.2685-0.24150.05620.7323-0.0618-0.03710.30.09620.469939.513268.53651.5146
23.33520.5250.03160.75170.05880.86460.00360.4675-0.0025-0.16750.0335-0.02790.07980.1076-0.03310.25790.03540.00030.27080.00450.190931.166833.466541.058
30.75050.00540.00041.24930.12791.943-0.0242-0.01660.13390.0383-0.0351-0.0843-0.30060.2230.05780.1951-0.06110.00160.22940.01790.239344.405254.357663.9035
40.4260.083-0.03862.4015-2.26953.1453-0.2814-0.0380.51140.1561-0.0358-0.08-0.76160.13160.34520.5578-0.0019-0.18010.2642-0.00110.48399.101365.153660.7615
54.44290.53510.32830.5753-0.01280.88830.0074-0.5442-0.08120.1157-0.0003-0.0359-0.0172-0.0701-0.00380.21860.0085-0.00210.24390.01240.18324.18835.070171.5295
64.77331.36540.22422.6318-2.13986.5167-0.0137-0.4709-0.34090.1607-0.0365-0.15510.1565-0.03650.0680.23790.0633-0.01830.1951-0.00670.283328.176124.892367.7395
76.564-3.001-1.09162.59790.44340.5617-0.01330.0366-0.2334-0.02750.00380.08710.07430.02830.02960.21410.0123-0.01980.20140.00840.179820.71828.307961.8866
81.99691.1321-1.04634.1935-2.92274.1956-0.35430.05790.4586-0.1346-0.0144-0.0869-0.62460.24910.27040.3904-0.0829-0.16830.21050.03120.444511.781761.18954.4028
90.0454-0.20590.00651.0403-0.1632.0341-0.23220.40630.265-0.29410.0377-0.2838-0.1170.45680.18070.4228-0.2221-0.09060.48110.15710.450116.141157.763841.9753
100.87670.05030.61340.86050.26111.8055-0.14980.12090.1767-0.16950.07240.1473-0.113-0.00020.06750.1852-0.0337-0.05510.16780.05110.25253.295246.657346.2131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 29 )A
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 169 )A
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 399 )A
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 29 )B
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 115 )B
6X-RAY DIFFRACTION6chain 'B' and (resid 116 through 139 )B
7X-RAY DIFFRACTION7chain 'B' and (resid 140 through 169 )B
8X-RAY DIFFRACTION8chain 'B' and (resid 170 through 214 )B
9X-RAY DIFFRACTION9chain 'B' and (resid 215 through 246 )B
10X-RAY DIFFRACTION10chain 'B' and (resid 247 through 399 )B

+
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