[English] 日本語
Yorodumi
- PDB-2z71: Structure of truncated mutant CYS1GLY of penicillin V acylase fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2z71
TitleStructure of truncated mutant CYS1GLY of penicillin V acylase from bacillus sphaericus co-crystallized with penicillin V
ComponentsPenicillin acylasePenicillin amidase
KeywordsHYDROLASE / ZYMOGEN / PRECURSOR / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE / CATALYSIS / PENICILLIN V ACYLASE
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / response to antibiotic
Similarity search - Function
Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PNV / Penicillin acylase
Similarity search - Component
Biological speciesBacillus sphaericus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
Citation
Journal: To be published
Title: Studies on the catalysis and post translational processing of penicillin V acylase
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#1: Journal: To be Published
Title: Auto-proteolytic processing of Penicillin V Acylase is simpler than of other related Ntn hydrolases
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#2: Journal: To be Published
Title: Co-crystal structure of Penicillin V Acylase with substrate Penicillin V: Insight in to catalytic specificity
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
#3: Journal: To be Published
Title: Polymorphism shown by the crystals of Penicillin V Acyalse from Bacillus sphaericus
Authors: Pathak, M.C. / Brannigan, J. / Dodson, G.G. / Suresh, C.G.
History
DepositionAug 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Penicillin acylase
C: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0994
Polymers74,3982
Non-polymers7012
Water91951
1
A: Penicillin acylase
C: Penicillin acylase
hetero molecules

A: Penicillin acylase
C: Penicillin acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1988
Polymers148,7964
Non-polymers1,4024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area21580 Å2
ΔGint-122 kcal/mol
Surface area44970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.730, 158.890, 90.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Penicillin acylase / Penicillin amidase / Penicillin V amidase / PVA


Mass: 37199.105 Da / Num. of mol.: 2 / Mutation: C1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sphaericus (bacteria) / Strain: NCIM 2478 / Production host: Escherichia coli (E. coli) / References: UniProt: P12256, penicillin amidase
#2: Chemical ChemComp-PNV / (2S,5R,6R)-3,3-DIMETHYL-7-OXO-6-(2-PHENOXYACETAMIDO)-4-THIA-1- AZABICYCLO(3.2.0)HEPTANE-2-CARBOXYLIC ACID / PENICILLIN V / Phenoxymethylpenicillin


Mass: 350.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18N2O5S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.4 / Details: pH 6.4, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorDate: Mar 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 78639 / Num. obs: 28157 / % possible obs: 89.6 %

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PVA

2pva


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 13.545 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2703 1320 5.1 %RANDOM
Rwork0.23881 ---
obs0.24045 24808 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.447 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å20 Å20 Å2
2---9.21 Å20 Å2
3---11.79 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 48 51 5260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0540.0225251
X-RAY DIFFRACTIONr_angle_refined_deg0.9791.9577139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5915659
X-RAY DIFFRACTIONr_chiral_restr0.1780.2814
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023953
X-RAY DIFFRACTIONr_nbd_refined0.2860.22565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_mcbond_it1.7171.53278
X-RAY DIFFRACTIONr_mcangle_it2.68225328
X-RAY DIFFRACTIONr_scbond_it4.01931973
X-RAY DIFFRACTIONr_scangle_it5.5474.51811
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.368 76
Rwork0.31 1362

+
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