[English] 日本語
Yorodumi
- PDB-2nlz: Crystal structure of cephalosporin acylase from Bacillus halodurans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2nlz
TitleCrystal structure of cephalosporin acylase from Bacillus halodurans
ComponentsCephalosporin acylase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ACYLASE / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics STRUCTURAL GENOMICS
Function / homology: / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal / Cephalosporin acylase
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.7 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of cephalosporin acylase from Bacillus halodurans
Authors: Patskovsky, Y. / Ramagopal, U. / Sauder, J.M. / Dickey, M. / Adams, J.M. / Ozyurt, S. / Wasserman, S.R. / Burley, S.K. / Almo, S.C.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / entity / entity_src_gen / entity_src_nat / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _entity.src_method / _struct_ref_seq_dif.details
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cephalosporin acylase
B: Cephalosporin acylase
C: Cephalosporin acylase
D: Cephalosporin acylase


Theoretical massNumber of molelcules
Total (without water)239,7494
Polymers239,7494
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14310 Å2
ΔGint-60 kcal/mol
Surface area66500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.745, 105.745, 385.062
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1VALVALAA3 - 5423 - 542
2METMETBB4 - 5424 - 542
3METMETCC4 - 5424 - 542
4METMETDD4 - 5444 - 544

-
Components

#1: Protein
Cephalosporin acylase


Mass: 59937.363 Da / Num. of mol.: 4 / Mutation: F170V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / References: UniProt: Q9KEI5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200MM SODIUM FORMATE, PH 7.5, 20% PEG 3350, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 23, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. all: 70277 / Num. obs: 70277 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.109 / Net I/σ(I): 6.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.03 / SU ML: 0.288 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24458 2011 3 %RANDOM
Rwork0.20982 ---
obs0.2109 64321 95.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16590 0 0 281 16871
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02217059
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.94823240
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36152149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50124.09775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.573152618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7711596
X-RAY DIFFRACTIONr_chiral_restr0.0930.22451
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213372
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1860.38111
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.511566
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.5960
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.3205
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.526
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7032.510846
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.2393.517123
X-RAY DIFFRACTIONr_scbond_it7.94647111
X-RAY DIFFRACTIONr_scangle_it10.85466110
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4122 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.1
2Btight positional0.080.1
3Ctight positional0.070.1
4Dtight positional0.080.1
1Atight thermal0.431.5
2Btight thermal0.41.5
3Ctight thermal0.431.5
4Dtight thermal0.411.5
LS refinement shellResolution: 2.7→2.769 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 107 -
Rwork0.332 4344 -
obs--88.97 %

+
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