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- PDB-3trg: Structure of an acylphosphatase from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3trg
TitleStructure of an acylphosphatase from Coxiella burnetii
ComponentsAcylphosphatase
KeywordsHYDROLASE / Fatty acid and phospholipid metabolism
Function / homology
Function and homology information


acylphosphatase / acylphosphatase activity
Similarity search - Function
Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Acylphosphatase signature 2. / Acylphosphatase / Acylphosphatase signature 1. / 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
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.601 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3853
Polymers11,2871
Non-polymers982
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.710, 69.710, 40.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-141-

HOH

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Components

#1: Protein Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 11287.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: acyP, CBU_1995 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83AB0, acylphosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 277 K / Method: sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate pH 5.6 0.2M ammonium acetate 30% PEG 4000, sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 23, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 14803 / Num. obs: 14789 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.048 / Χ2: 1.058 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.633.50.4417261.162199.9
1.63-1.663.60.3817481.3071100
1.66-1.693.70.3547081.117199.7
1.69-1.723.80.3157401.053199.9
1.72-1.763.90.277311.0281100
1.76-1.84.10.2337301.0061100
1.8-1.854.20.2127401.5151100
1.85-1.94.40.1767481.0641100
1.9-1.954.50.1347250.967199.9
1.95-2.024.60.1017420.8861100
2.02-2.094.70.0867220.8761100
2.09-2.175.10.0847471.0971100
2.17-2.275.80.0747441.2131100
2.27-2.3960.0667331.1091100
2.39-2.546.20.0587401.0231100
2.54-2.746.70.0527381.0011100
2.74-3.017.40.047470.9141100
3.01-3.459.20.037520.8391100
3.45-4.349.70.0277470.9961100
4.34-308.40.0317811.307199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.601→26.295 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8876 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 747 5.06 %RANDOM
Rwork0.1715 ---
all0.1723 15529 --
obs0.1723 14767 99.9 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.179 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 46.15 Å2 / Biso mean: 15.2615 Å2 / Biso min: 5.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.382 Å2-0 Å20 Å2
2---0.382 Å20 Å2
3---0.764 Å2
Refinement stepCycle: LAST / Resolution: 1.601→26.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 5 169 941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004802
X-RAY DIFFRACTIONf_angle_d0.871086
X-RAY DIFFRACTIONf_chiral_restr0.063120
X-RAY DIFFRACTIONf_plane_restr0.002140
X-RAY DIFFRACTIONf_dihedral_angle_d12.702295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6006-1.72420.30231450.257327712916
1.7242-1.89760.20561720.176927742946
1.8976-2.17210.18721400.159127932933
2.1721-2.73620.19121490.164728032952
2.7362-26.29850.16041410.162728793020
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)
10.28660.0228-0.08560.3138-0.31170.36060.0171-0.0688-0.00880.0966-0.01590.0035-0.13070.0614-0.00220.07570.00170.00510.0757-0.00190.05925.068412.4674-7.1371
20.1485-0.11620.01010.1297-0.02170.0830.01810.032-0.0198-0.0233-0.0010.0119-0.0285-0.0497-0.01720.06630.0217-0.0010.09040.00280.0813.446620.7405-16.7491
30.26830.3078-0.28880.6654-0.78771.28550.00370.03420.01310.01850.03540.0037-0.0607-0.1037-0.04190.0812-0.00370.01380.07330.00620.065519.565419.831-10.5075
40.2451-0.13950.03810.10220.00020.22660.00660.0444-0.0773-0.0129-0.00480.01480.02050.0296-0.00390.0644-0.001-0.00670.0794-0.00220.077321.380713.6111-16.9011
50.7212-0.51580.31540.395-0.21840.1432-0.1001-0.12720.03840.07320.0648-0.0201-0.087-0.07690.02850.10680.0259-0.0010.0991-0.00520.073822.741622.5906-5.6098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 18:35)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 36:51)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 52:60)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 61:101)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 102:112)A0

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