[English] 日本語
Yorodumi
- PDB-2x1d: The crystal structure of mature acyl coenzyme A:isopenicillin N a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x1d
TitleThe crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum
ComponentsACYL-COENZYME
KeywordsTRANSFERASE / ZYMOGEN / NTN-HYDROLASE / PENICILLIN BIOSYNTHESIS / ANTIBIOTIC BIOSYNTHESIS
Function / homology
Function and homology information


isopenicillin-N N-acyltransferase / isopenicillin-N N-acyltransferase activity / : / penicillin biosynthetic process / peroxisomal matrix
Similarity search - Function
Arc Repressor Mutant, subunit A - #2120 / : / Peptidase C45 / : / Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Orthogonal Bundle ...Arc Repressor Mutant, subunit A - #2120 / : / Peptidase C45 / : / Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (4S,5S)-1,2-DITHIANE-4,5-DIOL / PHOSPHATE ION / Isopenicillin-N N-acyltransferase
Similarity search - Component
Biological speciesPENICILLIUM CHRYSOGENUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBokhove, M. / Yoshida, H. / Hensgens, C.M.H. / van der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W.
CitationJournal: Structure / Year: 2010
Title: Structures of an Isopenicillin N Converting Ntn-Hydrolase Reveal Different Catalytic Roles for the Active Site Residues of Precursor and Mature Enzyme.
Authors: Bokhove, M. / Yoshida, H. / Hensgens, C.M.H. / Van Der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W.
History
DepositionDec 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACYL-COENZYME
B: ACYL-COENZYME
C: ACYL-COENZYME
D: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,07218
Polymers160,0934
Non-polymers97914
Water16,376909
1
A: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2464
Polymers40,0231
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2485
Polymers40,0231
Non-polymers2254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1183
Polymers40,0231
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4606
Polymers40,0231
Non-polymers4375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)198.711, 68.219, 146.964
Angle α, β, γ (deg.)90.00, 128.64, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
ACYL-COENZYME / ISOPENICILLIN-N N-ACYLTRANSFERASE / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 11 ...ISOPENICILLIN-N N-ACYLTRANSFERASE / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 11 KDA SUBUNIT / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 29 KDA SUBUNIT


Mass: 40023.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PENICILLIUM CHRYSOGENUM (fungus) / Strain: AS-P-78 / Plasmid: PKC787 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P15802, isopenicillin-N N-acyltransferase

-
Non-polymers , 6 types, 923 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growpH: 7 / Details: 1.95 M NA/KPO4 BUFFER, PH 6.9, 25MM NAOAC

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.64→40 Å / Num. obs: 187993 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.7
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X1C

2x1c


Resolution: 1.64→34.1 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.105 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20703 9288 5 %RANDOM
Rwork0.17944 ---
obs0.18083 175358 98.22 %-
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: 27.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.06 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.64→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11105 0 51 909 12065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.95115790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54951467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44523.627579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41151999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.54815102
X-RAY DIFFRACTIONr_chiral_restr0.0880.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219060
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.621.57180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.143211528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00534483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3954.54262
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: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 720 -
Rwork0.248 12819 -
obs--98.17 %
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)
11.14620.0901-0.09821.23240.17570.97380.08020.04160.0067-0.0184-0.04320.0570.0029-0.0824-0.0370.02350.00590.00250.055-0.00410.0375-31.60634.2762.826
21.41010.1860.19750.66360.07990.9922-0.05750.09820.11580.02530.0127-0.0288-0.1011-0.01240.04480.04560.0080.00870.01070.01410.0295-46.4249.9436.388
31.37640.24990.21870.7560.26241.20710.0543-0.0178-0.1628-0.0121-0.0012-0.01830.14930.1381-0.05320.06740.03010.01310.02140.00530.0388-17.79823.66858.104
40.6960.02820.13551.1576-0.12481.3315-0.0070.01880.00050.04020.0205-0.03830.05670.1238-0.01350.03220.0208-0.00030.0434-0.01770.04725.9628.67726.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 355
2X-RAY DIFFRACTION2B1 - 356
3X-RAY DIFFRACTION3C1 - 356
4X-RAY DIFFRACTION4D1 - 355

+
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