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- PDB-1ghd: Crystal structure of the glutaryl-7-aminocephalosporanic acid acy... -

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Basic information

Entry
Database: PDB / ID: 1ghd
TitleCrystal structure of the glutaryl-7-aminocephalosporanic acid acylase by mad phasing
Components(GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE) x 2
KeywordsHYDROLASE / cephalosporin acylase
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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 / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cephalosporin acylase
Similarity search - Component
Biological speciesPseudomonas sp. 130 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsDing, Y. / Jiang, W. / Mao, X. / He, H. / Zhang, S. / Tang, H. / Bartlam, M. / Ye, S. / Jiang, F. / Liu, Y. ...Ding, Y. / Jiang, W. / Mao, X. / He, H. / Zhang, S. / Tang, H. / Bartlam, M. / Ye, S. / Jiang, F. / Liu, Y. / Zhao, G. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Affinity alkylation of the Trp-B4 residue of the beta -subunit of the glutaryl 7-aminocephalosporanic acid acylase of Pseudomonas sp. 130.
Authors: Huang, X. / Zeng, R. / Ding, X. / Mao, X. / Ding, Y. / Rao, Z. / Xie, Y. / Jiang, W. / Zhao, G.
History
DepositionDec 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE
B: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE


Theoretical massNumber of molelcules
Total (without water)77,5932
Polymers77,5932
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-54 kcal/mol
Surface area24380 Å2
MethodPISA
2
A: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE
B: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE

A: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE
B: GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE


Theoretical massNumber of molelcules
Total (without water)155,1864
Polymers155,1864
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area17600 Å2
ΔGint-118 kcal/mol
Surface area46860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.48, 73.48, 382.02
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE


Mass: 18737.322 Da / Num. of mol.: 1 / Fragment: ALPHA-SUBUNIT + SPACER PEPTIDE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 130 (bacteria) / Plasmid: PMFT7H6CAII / Production host: Escherichia coli (E. coli)
References: UniProt: O86089, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein GLUTARYL-7-AMINOCEPHALOSPORANIC ACID ACYLASE


Mass: 58855.785 Da / Num. of mol.: 1 / Fragment: BETA-SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. 130 (bacteria) / Plasmid: PMFT7H6CAII / Production host: Escherichia coli (E. coli)
References: UniProt: O86089, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.98 %
Crystal growTemperature: 291 K / Method: hanging drop/vapor diffusion / pH: 7.5
Details: sodium acetate, cadmium sulfate, hepes, pH 7.5, HANGING DROP/VAPOR DIFFUSION, temperature 291.0K
Crystal grow
*PLUS
Method: unknown / Details: Ichikawa, S., (1981) Agric. Biol. Chem., 45, 2231.

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9639
DetectorType: SBC-2 / Detector: CCD / Date: Nov 8, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9639 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 69082 / Num. obs: 68105 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 30.5
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.48 / Num. unique all: 5097 / % possible all: 97.1

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Processing

Software
NameVersionClassification
DENZO2000data reduction
SCALEPACK2000data scaling
O7model building
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.265 7585 -
Rwork0.218 --
all-78107 -
obs-76374 97.8 %
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 0 198 5504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.29

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