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- PDB-7chx: acylphosphatase from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 7chx
Titleacylphosphatase from Staphylococcus aureus
ComponentsAcylphosphatase
KeywordsSTRUCTURAL PROTEIN / acylphosphatase
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity / carboxyl- or carbamoyltransferase activity / protein maturation / zinc ion binding
Similarity search - Function
: / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.49 Å
AuthorsLee, K.-Y. / Kim, D.-G. / Lee, B.-J.
Funding support Korea, Republic Of, 4items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2018R1A2A1A19018526 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2016R1C1B2014609 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019R1H1A1102102 Korea, Republic Of
CitationJournal: To Be Published
Title: acylphosphatase from Staphylococcus aureus
Authors: Lee, K.-Y.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylphosphatase
B: Acylphosphatase


Theoretical massNumber of molelcules
Total (without water)24,4112
Polymers24,4112
Non-polymers00
Water2,054114
1
A: Acylphosphatase


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acylphosphatase


Theoretical massNumber of molelcules
Total (without water)12,2061
Polymers12,2061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.124, 77.124, 35.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Acylphosphatase


Mass: 12205.601 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: acyP, yccX, BN1321_260044, BTN44_05560, DDL17_12795, DQV20_10240, DQV53_07555, E4U00_04725, EP54_14800, EQ90_12880, ERS072840_02314, FA040_08725, FVP29_18130, GIX97_03140, GO677_08310, GO706_ ...Gene: acyP, yccX, BN1321_260044, BTN44_05560, DDL17_12795, DQV20_10240, DQV53_07555, E4U00_04725, EP54_14800, EQ90_12880, ERS072840_02314, FA040_08725, FVP29_18130, GIX97_03140, GO677_08310, GO706_12140, GO746_10695, GO793_05135, GO803_14910, GO805_11030, GO810_04440, GO894_09605, GO941_00230, HMPREF3211_00435, M1K003_0247, NCTC10654_01455, NCTC10702_02217, NCTC5664_03214, NCTC6133_01806, NCTC7878_01640, NCTC9944_01419, RK64_07545, SAMEA1469856_01199, SAMEA1469884_02272, SAMEA1531680_02336, SAMEA1531701_02465, SAMEA2080329_01054, SAMEA2080330_01500, SAMEA2080334_01727, SAMEA2080433_01274, SAST44_01480, SAST45_01515
Production host: Escherichia coli (E. coli) / References: UniProt: W8U612, acylphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris, pH 8.5, 30% (w/v) PEG4000, 200 mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.49→30 Å / Num. obs: 32259 / % possible obs: 94.1 % / Redundancy: 3.5 % / CC1/2: 0.984 / Net I/σ(I): 26.94
Reflection shellResolution: 1.49→1.52 Å / Num. unique obs: 1417 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: SAD / Resolution: 1.49→25.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.461 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 1647 5.1 %RANDOM
Rwork0.201 ---
obs0.2031 30595 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.68 Å2 / Biso mean: 22.39 Å2 / Biso min: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.91 Å2
Refinement stepCycle: final / Resolution: 1.49→25.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1474 0 0 114 1588
Biso mean---36.2 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131500
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171336
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6342024
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5753080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0765180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18922.115104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5215252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4211514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
X-RAY DIFFRACTIONr_rigid_bond_restr2.0932836
LS refinement shellResolution: 1.493→1.532 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 129 -
Rwork0.311 2285 -
all-2414 -
obs--97.42 %

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