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- PDB-1d2t: CRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE -

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Basic information

Entry
Database: PDB / ID: 1d2t
TitleCRYSTAL STRUCTURE OF ACID PHOSPHATASE FROM ESCHERICHIA BLATTAE
ComponentsACID PHOSPHATASE
KeywordsHYDROLASE / ALL ALPHA
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / Vanadium-containing Chloroperoxidase; domain 1 / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEscherichia blattae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsIshikawa, K. / Mihara, Y. / Gondoh, K. / Suzuki, E. / Asano, Y.
CitationJournal: EMBO J. / Year: 2000
Title: X-ray structures of a novel acid phosphatase from Escherichia blattae and its complex with the transition-state analog molybdate.
Authors: Ishikawa, K. / Mihara, Y. / Gondoh, K. / Suzuki, E. / Asano, Y.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1292
Polymers25,0331
Non-polymers961
Water4,252236
1
A: ACID PHOSPHATASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)150,77512
Polymers150,1996
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_556-x+y,y,-z+3/21
crystal symmetry operation12_566x,x-y+1,-z+3/21
Buried area13060 Å2
ΔGint-201 kcal/mol
Surface area48800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.700, 124.700, 97.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ACID PHOSPHATASE


Mass: 25033.098 Da / Num. of mol.: 1 / Fragment: ACID PHOSPHATASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia blattae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S1A6, acid phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG400, TRIS, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
343-45 %PEG4001reservoir
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. all: 35216 / Num. obs: 33066 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.72
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.341 / % possible all: 74.4
Reflection
*PLUS
Num. obs: 34749 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 74.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
MLPHAREphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementResolution: 1.9→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.257 29341 -RANDOM
Rwork0.216 ---
all0.219 34749 --
obs0.215 32601 92.7 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 5 236 1937
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d0.017
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.988
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_d

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