[English] 日本語
Yorodumi
- PDB-1k5s: PENICILLIN ACYLASE, MUTANT COMPLEXED WITH PPA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k5s
TitlePENICILLIN ACYLASE, MUTANT COMPLEXED WITH PPA
Components
  • PENICILLIN G ACYLASE ALPHA SUBUNIT
  • PENICILLIN G ACYLASE BETA SUBUNIT
KeywordsHYDROLASE / NTN-HYDROLASE FOLD / HELICES / BETA-STRANDS
Function / homology
Function and homology information


penicillin amidase activity / penicillin amidase / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase ...Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
R-2-PHENYL-PROPRIONIC ACID / Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHensgens, C.M.H. / Keizer, E. / Snijder, H.J. / Dijkstra, B.W.
CitationJournal: Protein Eng.Des.Sel. / Year: 2004
Title: Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase.
Authors: Alkema, W.B.L. / Hensgens, C.M.H. / Snijder, H.J. / Keizer, E. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionOct 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 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 G ACYLASE ALPHA SUBUNIT
B: PENICILLIN G ACYLASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3974
Polymers86,2062
Non-polymers1902
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-94 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.820, 64.360, 64.750
Angle α, β, γ (deg.)72.89, 74.01, 73.55
Int Tables number1
Space group name H-MP1
DetailsThe alpha and beta unit together form the biological unit / the alpha and beta unit together form the biological relevant unit

-
Components

#1: Protein PENICILLIN G ACYLASE ALPHA SUBUNIT / PENICILLIN G AMIDASE / PENICILLIN G AMIDOHYDROLASE


Mass: 23838.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAC / Plasmid: PEC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P06875, penicillin amidase
#2: Protein PENICILLIN G ACYLASE BETA SUBUNIT / PENICILLIN G AMIDASE / PENICILLIN G AMIDOHYDROLASE


Mass: 62367.426 Da / Num. of mol.: 1 / Mutation: F24A, V148L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAC / Plasmid: PEC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P06875, penicillin amidase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GRO / R-2-PHENYL-PROPRIONIC ACID


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.11 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: MOPS BUFFER, PEG MME 2K, PPA, pH 7.20, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14-10 mg/mlprotein1drop
250 mMMOPS1droppH7.2
350 mMMOPS1reservoirpH7.2
412-20 %(w/v)PEG2000 MME1reservoir

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Jan 1, 2000 / 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: 2.43→30 Å / Num. all: 27684 / Num. obs: 26632 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.185 % / Rsym value: 0.037 / Net I/σ(I): 21.1
Reflection shellResolution: 2.43→2.47 Å / Mean I/σ(I) obs: 10.9 / Rsym value: 0.066 / % possible all: 95.7
Reflection
*PLUS
Highest resolution: 2.43 Å / Lowest resolution: 30 Å / Num. measured all: 58181 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 10.9

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMAC5refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PNK

1pnk


Resolution: 2.43→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1375 5.2 %RANDOM
Rwork0.173 ---
obs0.194 26632 96.2 %-
Displacement parametersBiso mean: 18.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20.06 Å2-0.23 Å2
2--0.14 Å2-0.36 Å2
3---0.6 Å2
Refine analyzeLuzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 12 360 6439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d1.131
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.215
X-RAY DIFFRACTIONp_mcbond_it0.629
X-RAY DIFFRACTIONp_mcangle_it1.049
X-RAY DIFFRACTIONp_scbond_it1.569
X-RAY DIFFRACTIONp_scangle_it2.261
X-RAY DIFFRACTIONp_plane_restr0.004
X-RAY DIFFRACTIONp_chiral_restr0.075
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.139
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellHighest resolution: 2.43 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.173 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.131
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.787

+
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