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- PDB-4hi2: Crystal structure of an Acylphosphatase protein cage -

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Basic information

Entry
Database: PDB / ID: 4hi2
TitleCrystal structure of an Acylphosphatase protein cage
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
Biological speciesVibrio cholerae O395 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: Acylphosphatase
C: Acylphosphatase
D: Acylphosphatase
E: Acylphosphatase
F: Acylphosphatase
G: Acylphosphatase
H: Acylphosphatase
I: Acylphosphatase
J: Acylphosphatase
K: Acylphosphatase
L: Acylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,99455
Polymers122,86312
Non-polymers4,13143
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.940, 104.940, 147.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Acylphosphatase / Acylphosphate phosphohydrolase


Mass: 10238.567 Da / Num. of mol.: 12
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: SO4

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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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.6M AMS, 0.1M HEPES, pH=7.0, 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: 3.1→28.18 Å / Num. obs: 31972 / % possible obs: 96.8 % / Redundancy: 1.8 %
Reflection shellHighest resolution: 3.1 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 5.8 / % possible all: 96.8

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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: 3.1→28.178 Å / SU ML: 0.5 / σ(F): 1.96 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2891 1606 5.04 %Random
Rwork0.2209 ---
obs0.2244 31837 96.52 %-
all-31972 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 3.1→28.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8333 0 215 0 8548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098685
X-RAY DIFFRACTIONf_angle_d1.3411738
X-RAY DIFFRACTIONf_dihedral_angle_d18.6743093
X-RAY DIFFRACTIONf_chiral_restr0.0831238
X-RAY DIFFRACTIONf_plane_restr0.0051501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.20010.34731560.29352746X-RAY DIFFRACTION97
3.2001-3.31430.31141540.26542750X-RAY DIFFRACTION98
3.3143-3.44670.35911690.27822801X-RAY DIFFRACTION99
3.4467-3.60330.38621380.31862835X-RAY DIFFRACTION99
3.6033-3.79290.63641190.44982599X-RAY DIFFRACTION91
3.7929-4.02990.31671490.27062827X-RAY DIFFRACTION98
4.0299-4.340.20281450.16062778X-RAY DIFFRACTION98
4.34-4.77480.18331450.12332807X-RAY DIFFRACTION98
4.7748-5.46140.19611480.13182745X-RAY DIFFRACTION97
5.4614-6.86430.24411480.17912716X-RAY DIFFRACTION96
6.8643-28.17890.24261350.17152627X-RAY DIFFRACTION92
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)
11.4377-1.42780.29311.7964-1.44191.9404-0.3730.0319-0.14170.0369-0.04410.1296-0.0052-0.4286-0.05360.5305-0.18390.08080.33690.02840.542-15.084322.9962-12.5313
20.07390.00740.0927-0.03090.01230.09110.0439-0.1565-0.03160.15-0.0825-0.0359-0.4203-0.2933-00.65580.0635-0.05370.36750.00520.6196-19.956145.8479-26.556
30.6281-0.3194-0.54151.24881.30151.2890.2383-0.1250.08160.1327-0.1920.15890.36940.0056-0.00210.4762-0.1102-0.07730.3464-0.01090.42811.401844.5112-9.3613
42.541-1.60470.59530.9267-0.41460.5792-0.1564-0.24260.05360.29760.1528-0.11420.01210.31350.00010.51540.0284-0.090.6335-0.06160.503818.706622.2036-12.7436
51.3265-0.7625-1.12391.1964-0.0061.39950.01390.0115-0.1238-0.2802-0.0805-0.37010.31050.2246-0.00050.55230.16090.0320.5033-0.08570.579323.45414.3563-38.411
61.4259-0.64510.95311.21130.53021.46480.3039-0.2791-0.2353-0.04580.01830.13170.18650.22460.00360.72080.03710.12970.29490.06120.53742.19964.0739-24.6422
72.13231.53070.00371.355-0.57691.0762-0.33640.29930.0017-0.14250.3486-0.1166-0.12180.49170.00020.5813-0.04210.09590.5482-0.04310.51218.738538.3525-52.7992
81.48041.07781.00751.24990.33780.8628-0.11080.06140.1806-0.0544-0.0847-0.1427-0.34220.4535-0.00050.5107-0.1161-0.0450.5646-0.06430.54923.470246.2363-27.1023
91.46310.7975-0.7091.66851.06551.86760.01690.2150.23670.00170.03030.1508-0.45970.248600.6680.0082-0.10960.27390.03440.51372.231756.5323-40.8939
100.54960.8711-0.15272.3267-1.86542.2503-0.2977-0.03090.07770.0680.07840.0975-0.2783-0.3204-0.01880.45020.1639-0.08020.38060.04650.4764-15.052437.5759-53.0195
111.28820.40830.52060.13960.03841.35-0.17710.2249-0.1151-0.0025-0.04530.08670.4584-0.3995-0.00050.7167-0.08520.03940.26740.04140.628-19.957714.716-38.9987
121.4-0.62041.01380.83140.28381.30720.15250.1639-0.0995-0.1474-0.04020.1317-0.02420.158-0.00050.58820.10860.07510.3101-0.02460.42811.470416.0997-56.1841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:91)
2X-RAY DIFFRACTION2(chain B and resid 3:91)
3X-RAY DIFFRACTION3(chain C and resid 4:91)
4X-RAY DIFFRACTION4(chain D and resid 4:91)
5X-RAY DIFFRACTION5(chain E and resid 4:91)
6X-RAY DIFFRACTION6(chain F and resid 4:91)
7X-RAY DIFFRACTION7(chain G and resid 4:91)
8X-RAY DIFFRACTION8(chain H and resid 4:91)
9X-RAY DIFFRACTION9(chain I and resid 4:91)
10X-RAY DIFFRACTION10(chain J and resid 4:91)
11X-RAY DIFFRACTION11(chain K and resid 3:91)
12X-RAY DIFFRACTION12(chain L and resid 4:91)

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