[English] 日本語
Yorodumi
- PDB-2iwm: precursor mutant Cys1Ser of Penicillin V Acylase from Bacillus sp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iwm
Titleprecursor mutant Cys1Ser of Penicillin V Acylase from Bacillus sphaericus
ComponentsPENICILLIN ACYLASEPenicillin amidase
KeywordsHYDROLASE / ZYMOGEN / PRECURSOR / PENICILLIN / AUTOPROTEOLYSIS / ANTIBIOTIC RESISTANCE
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
Biological speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChandra, P.M. / Dodson, G. / Suresh, C.G.
Citation
Journal: To be Published
Title: Precursor Mutant Cys1Ser of Penicillin V Acylase from Bacilus Sphaericus
Authors: Chandra, P.M. / Brannigan, J. / Prabhune, A. / Pundle, A. / Turkenburg, J. / Dodson, G. / Suresh, C.G.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2004
Title: Cloning, Preparation and Preliminary Crystallographic Studies of Penicillin V Acylase Autoproteolytic Processing Mutants
Authors: Chandra, P.M. / Brannigan, J. / Prabhune, A. / Pundle, A. / Turkenburg, J. / Dodson, G. / Suresh, C.G.
History
DepositionJul 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PENICILLIN ACYLASE
B: PENICILLIN ACYLASE
C: PENICILLIN ACYLASE
D: PENICILLIN ACYLASE


Theoretical massNumber of molelcules
Total (without water)150,1224
Polymers150,1224
Non-polymers00
Water5,819323
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21790 Å2
ΔGint-142.3 kcal/mol
Surface area55870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)102.642, 90.089, 102.269
Angle α, β, γ (deg.)90.00, 102.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
PENICILLIN ACYLASE / Penicillin amidase / CYS1SER PRECURSOR MUTANT OF PENICILLIN V ACYLASE / PENICILLIN V AMIDASE / PVA


Mass: 37530.535 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CYS 4 HAS BEEN MUTATED TO SER BY SITE DIRECTED MUTAGENESIS. RESIDUE CYS1 IN NATIVE PVA IS CYS4 IN THE PRECURSOR STRUCTURE BECAUSE OF ADDITIONAL TRI-PEPTIDE AT N-TERMINUS
Source: (gene. exp.) BACILLUS SPHAERICUS (bacteria) / Description: BACILLUS SPHAERICUS NCIM 2478 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P12256, penicillin amidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 4 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 4 TO SER ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, CYS 4 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 4 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 4 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 4 TO SER

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growpH: 6.4
Details: 700 MICRO LITRE PHOSPHATE BUFFER PH 6.4, 300 MICRO LITRE SATURATED AMMONIUM SULPHATE, 100 MICRO LITRE SUCROSE, 50 MICRO LITRE DMSO

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: May 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 62997 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 3.74 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5

-
Processing

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

2pva


Resolution: 2.5→100 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.943 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3170 5 %RANDOM
Rwork0.201 ---
obs0.203 59797 99.8 %-
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: 27.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.03 Å2
2---0.09 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10410 0 0 323 10733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02210626
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.95814440
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80651330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.21648
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027980
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.35145
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.5881
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.56622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.375210770
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02934004
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3164.53670
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.287 227
Rwork0.233 4257
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)
10.3284-0.1457-0.20110.23560.01680.92850.0212-0.0634-0.02970.05410.013-0.0038-0.15340.0043-0.03420.1334-0.0230.06040.21470.01070.052553.09345.11669.429
20.32870.0958-0.21670.1670.01261.3440.02120.0948-0.0478-0.0690.0032-0.0081-0.1385-0.0187-0.02440.140.02240.06070.2262-0.00720.027651.75744.32615.515
31.1197-0.14430.02380.1448-0.01520.57850.02840.0249-0.1029-0.0369-0.0340.0784-0.0459-0.16920.00560.05860.04930.04080.2401-0.01430.094425.98242.24436.243
41.1573-0.07350.00460.19940.02240.37580.03120.0176-0.09350.0014-0.0253-0.0566-0.06340.1158-0.00580.0523-0.0260.04690.2319-0.0010.112278.45240.29848.772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 331
2X-RAY DIFFRACTION2B1 - 331
3X-RAY DIFFRACTION3C1 - 331
4X-RAY DIFFRACTION4D1 - 331

+
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