[English] 日本語
Yorodumi
- PDB-6c0d: Crystal structure of an Amidase (hydantoinase/carbamoylase family... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c0d
TitleCrystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum
ComponentsAmidase, hydantoinase/carbamoylase family
KeywordsHYDROLASE / SSGCID / Structural genomics / Burkholderia phymatum / amidase / hydrantoinase family / carbamoylase family / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Bacterial exopeptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Amidase, hydantoinase/carbamoylase family
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an Amidase (hydantoinase/carbamoylase family) from Burkholderia phymatum
Authors: Abendroth, J. / Conrady, D.G. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amidase, hydantoinase/carbamoylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,29912
Polymers45,3681
Non-polymers93011
Water8,701483
1
A: Amidase, hydantoinase/carbamoylase family
hetero molecules

A: Amidase, hydantoinase/carbamoylase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,59724
Polymers90,7372
Non-polymers1,86122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area7950 Å2
ΔGint-97 kcal/mol
Surface area31010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.620, 136.620, 67.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

21A-1083-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Amidase, hydantoinase/carbamoylase family /


Mass: 45368.262 Da / Num. of mol.: 1 / Fragment: BuphA.12245.b.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_4610 / Plasmid: BuphA.12245.b.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2JR29, N-carbamoyl-L-amino-acid hydrolase

-
Non-polymers , 5 types, 494 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 4.01 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG-1 screen F11: 200mM Ammonium sulfate, 25% PEG 3350, 100mM HEPES free acid / NaOH pH 7.5: BuphA.12245.b.B1.PW38373 at 22.42mg/ml: cryo: 15% EG in 2 steps: tray 296390 f11: puck jzk7-6.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→44.719 Å / Num. obs: 67274 / % possible obs: 100 % / Redundancy: 7.405 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.067 / Χ2: 1.066 / Net I/σ(I): 17.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.854.4320.5452.0849470.8280.62100
1.85-1.94.5970.4572.5747940.8910.518100
1.9-1.954.7660.3623.3347140.9290.407100
1.95-2.014.9390.2854.5145200.950.319100
2.01-2.085.1070.235.8443940.9660.25699.9
2.08-2.155.7070.1828.1442770.9820.201100
2.15-2.236.7260.16310.4141300.9880.177100
2.23-2.327.0860.14212.1539760.9910.154100
2.32-2.437.4890.12514.2138150.9940.13599.9
2.43-2.557.9650.10816.8736280.9950.11699.9
2.55-2.688.6450.09420.1234750.9970.199.9
2.68-2.8510.0760.08125.3332860.9980.085100
2.85-3.0410.8710.07229.0431110.9980.075100
3.04-3.2910.8550.06133.5628750.9990.065100
3.29-3.610.7670.05138.9326760.9990.054100
3.6-4.0210.660.04743.3124240.9990.049100
4.02-4.6510.6250.04345.6221440.9990.045100
4.65-5.6910.7720.03945.8218310.9990.041100
5.69-8.0510.80.03744.3114330.9990.039100
8.05-44.71910.1410.03148.518240.9990.03299

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
PHENIX1.13rc1_2961refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5j4mA as per MorDa

Resolution: 1.8→44.719 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.56
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 1991 2.96 %0
Rwork0.1574 ---
obs0.158 67230 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.81 Å2 / Biso mean: 32.1336 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.8→44.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 58 500 3571
Biso mean--56.88 43.46 -
Num. residues----404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.84510.26461340.226546404774
1.8451-1.8950.19911440.209946244768
1.895-1.95080.22271450.196946254770
1.9508-2.01370.22391690.177345644733
2.0137-2.08570.19891680.163946394807
2.0857-2.16920.17391620.158246024764
2.1692-2.26790.19771460.165346144760
2.2679-2.38750.19951290.163446474776
2.3875-2.5370.20451090.16746964805
2.537-2.73290.17041600.159246284788
2.7329-3.00790.18181450.16246624807
3.0079-3.4430.19441000.151347234823
3.443-4.33720.13141190.13347394858
4.3372-44.73320.16091610.147848364997
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)
11.8647-0.2235-0.03841.89330.0313.144-0.0003-0.00270.4069-0.1915-0.0201-0.1018-0.76070.0763-0.00130.3077-0.00690.00160.1406-0.00480.251463.085364.13939.3074
22.40491.2036-1.0650.6264-0.50950.46240.1222-0.22490.08140.0681-0.08070.0001-0.09350.1806-0.04360.1487-0.04980.00920.2164-0.00290.167995.875360.37660.3062
32.50930.18660.24941.52391.07012.1382-0.03430.07490.1515-0.23680.0009-0.0132-0.30550.21760.03150.1427-0.01160.00120.12570.02430.14367.399450.24176.6279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 198 )A3 - 198
2X-RAY DIFFRACTION2chain 'A' and (resid 199 through 345 )A199 - 345
3X-RAY DIFFRACTION3chain 'A' and (resid 346 through 413 )A346 - 413

+
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