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- PDB-4hi1: Crystal structure of acylphosphatase C20R mutant from Vibrio chol... -

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Basic information

Entry
Database: PDB / ID: 4hi1
TitleCrystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395
ComponentsAcylphosphatase
KeywordsHYDROLASE / Ferredoxin fold
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MOLYBDATE ION / Acylphosphatase
Similarity search - Component
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.964 Å
AuthorsNath, S. / Banerjee, R. / Sen, U.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal structure of acylphosphatase C20R mutant from Vibrio cholerae0395
Authors: Nath, S. / Banerjee, R. / Sen, U.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acylphosphatase
B: Acylphosphatase
C: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6469
Polymers30,8783
Non-polymers7686
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-46.9 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.710, 81.300, 40.530
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10292.619 Da / Num. of mol.: 3 / Mutation: C20R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O395 (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: acyP, VC0395_A0969, VC395_1474 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5F8G9, acylphosphatase
#2: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE


Mass: 159.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: MoO4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6M ammonium sulfate, 0.1M bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2012
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.964→39.708 Å / Num. obs: 17237 / % possible obs: 93.5 %
Reflection shellResolution: 1.96→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 12.5 / Num. unique all: 17237 / % possible all: 93.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BJD

2bjd


Resolution: 1.964→39.708 Å / SU ML: 0.23 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 872 5.07 %RANDOM
Rwork0.1874 ---
obs0.1907 17218 90.52 %-
all-17218 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.964→39.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2045 0 30 249 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112131
X-RAY DIFFRACTIONf_angle_d1.3282879
X-RAY DIFFRACTIONf_dihedral_angle_d15.327775
X-RAY DIFFRACTIONf_chiral_restr0.08306
X-RAY DIFFRACTIONf_plane_restr0.005372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9642-2.0220.29011430.21032715X-RAY DIFFRACTION94
2.022-2.08730.29411200.22182028X-RAY DIFFRACTION71
2.0873-2.16190.28291390.20372708X-RAY DIFFRACTION95
2.1619-2.24850.45891340.29582670X-RAY DIFFRACTION94
2.2485-2.35080.3719960.21552108X-RAY DIFFRACTION95
2.3508-2.47470.26081450.20382786X-RAY DIFFRACTION96
2.4747-2.62970.28151380.20322742X-RAY DIFFRACTION97
2.6297-2.83270.28291290.19122522X-RAY DIFFRACTION87
2.8327-3.11770.291510.19472800X-RAY DIFFRACTION98
3.1177-3.56860.23421650.16532609X-RAY DIFFRACTION92
3.5686-4.4950.15651530.14162553X-RAY DIFFRACTION90
4.495-39.71650.18751460.16782839X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 34.199 Å / Origin y: 27.7704 Å / Origin z: 20.3423 Å
111213212223313233
T0.0591 Å2-0.01 Å20.0155 Å2-0.0565 Å20.0039 Å2--0.0754 Å2
L0.6003 °2-0.084 °2-0.0446 °2-0.8396 °20.2407 °2--0.8878 °2
S0.0245 Å °0.0023 Å °0.0485 Å °0.0265 Å °-0.029 Å °0.085 Å °0.0052 Å °-0.0268 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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