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- PDB-2bje: Acylphosphatase from Sulfolobus solfataricus. Monclinic P21 space... -

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Basic information

Entry
Database: PDB / ID: 2bje
TitleAcylphosphatase from Sulfolobus solfataricus. Monclinic P21 space group
ComponentsACYLPHOSPHATASE
KeywordsHYDROLASE
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 speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRosano, C. / Zuccotti, S.
Citation
Journal: Proteins: Struct., Funct., Bioinf. / Year: 2006
Title: Structure, Conformational Stability, and Enzymatic Properties of Acylphosphatase from the Hyperthermophile Sulfolobus Solfataricus.
Authors: Corazza, A. / Rosano, C. / Pagano, K. / Alverdi, V. / Esposito, G. / Capanni, C. / Bemporad, F. / Plakoutsi, G. / Stefani, M. / Chiti, F. / Zuccotti, S. / Bolognesi, M. / Viglino, P.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Preliminary Characterization of Two Different Crystal Forms of Acylphosphatase from the Hyperthermophile Archaeon Sulfolobus Solfataricus
Authors: Zuccotti, S. / Rosano, C. / Bemporad, F. / Stefani, M. / Bolognesi, M.
History
DepositionFeb 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACYLPHOSPHATASE
C: ACYLPHOSPHATASE
E: ACYLPHOSPHATASE
G: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,22111
Polymers46,6094
Non-polymers6127
Water3,315184
1
A: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9765
Polymers11,6521
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7482
Polymers11,6521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7482
Polymers11,6521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: ACYLPHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7482
Polymers11,6521
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.980, 56.532, 60.805
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ACYLPHOSPHATASE


Mass: 11652.300 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97ZL0, acylphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.87 Å3/Da / Density % sol: 33.65 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→29.54 Å / Num. obs: 25338 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACY

2acy


Resolution: 1.9→8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.231 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1266 5.1 %RANDOM
Rwork0.162 ---
obs0.166 23644 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-1.24 Å2
2--0.79 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 31 184 3115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223030
X-RAY DIFFRACTIONr_bond_other_d00.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.9914073
X-RAY DIFFRACTIONr_angle_other_deg0.90436224
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.94423.758149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.86315541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3381520
X-RAY DIFFRACTIONr_chiral_restr0.150.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.020.022312
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02632
X-RAY DIFFRACTIONr_nbd_refined0.2660.21382
X-RAY DIFFRACTIONr_nbd_other0.3140.21010
X-RAY DIFFRACTIONr_nbtor_refined0.3480.22066
X-RAY DIFFRACTIONr_nbtor_other0.0920.21996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2510.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3330.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7991.51861
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6122875
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3731337
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.51131198
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.245 167
Rwork0.18 3218
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)
12.5131.5574-0.90476.8239-1.20454.92970.1170.02650.05540.1482-0.16780.1009-0.09120.09150.0508-0.163-0.01210.1351-0.30480.0031-0.24422.0420.7347.411
21.39540.5841-1.10234.43342.21498.02260.00170.0695-0.15140.01970.0407-0.26890.19830.0488-0.0423-0.17590.0060.1105-0.2903-0.0056-0.18528.044.211-22.881
32.0017-0.2758-1.39063.80982.57088.0161-0.15020.0153-0.01990.02750.06040.03370.0584-0.20280.0897-0.1743-0.00550.1164-0.2443-0.0206-0.204920.801-3.37724.513
43.2912-3.5592-0.06599.3669-1.14633.9751-0.02-0.0752-0.02980.29680.0270.16860.0091-0.1523-0.007-0.09720.02010.1206-0.26420.0019-0.235928.4630.205-5.438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 94
2X-RAY DIFFRACTION2C4 - 94
3X-RAY DIFFRACTION3E4 - 94
4X-RAY DIFFRACTION4G4 - 94

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