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- PDB-3rqz: Crystal structure of metallophosphoesterase from Sphaerobacter th... -

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Basic information

Entry
Database: PDB / ID: 3rqz
TitleCrystal structure of metallophosphoesterase from Sphaerobacter thermophilus
ComponentsMetallophosphoesterase
KeywordsHYDROLASE / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / phosphoesterase / ZN binding
Function / homology
Function and homology information


Phosphoesterase MJ0912 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Metallophosphoesterase
Similarity search - Component
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of metallophosphoesterase from Sphaerobacter thermophilus
Authors: Chang, C. / Wu, R. / Clancy, S. / Joachimiak, A.
History
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,26210
Polymers82,8103
Non-polymers4517
Water4,972276
1
A: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7343
Polymers27,6031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7343
Polymers27,6031
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Metallophosphoesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7934
Polymers27,6031
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.838, 72.838, 123.006
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Metallophosphoesterase


Mass: 27603.463 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / S 6022 / Gene: Sthe_1642 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D1C4A9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M Calcium acetate, 0.1M MES pH 6.0, 10% 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.789
11-H, H+K, -L20.088
11-h,-k,l30.123
ReflectionResolution: 1.95→50 Å / Num. all: 53258 / Num. obs: 53210 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 31.5
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 2.42 / Num. unique all: 2641 / % possible all: 98.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.735 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1504 2726 5.1 %RANDOM
Rwork0.1235 ---
all0.1249 53112 --
obs0.1249 53112 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.84 Å2 / Biso mean: 34.1809 Å2 / Biso min: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2---1.58 Å20 Å2
3---3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 10 276 5986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215963
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9428172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78322.925294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53315879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.641558
X-RAY DIFFRACTIONr_chiral_restr0.0940.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214737
X-RAY DIFFRACTIONr_mcbond_it1.2731.53702
X-RAY DIFFRACTIONr_mcangle_it2.19926002
X-RAY DIFFRACTIONr_scbond_it3.20832261
X-RAY DIFFRACTIONr_scangle_it4.9554.52170
X-RAY DIFFRACTIONr_rigid_bond_restr1.65935963
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 186 -
Rwork0.147 3637 -
all-3823 -
obs-3823 97.03 %
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)
10.2395-0.0184-0.06940.06260.03970.220.0007-0.00140.0051-0.00080.0021-0.002-0.00660.0085-0.00280.00570.0002-0.00180.0049-0.00030.023912.565825.8371-0.0956
20.1649-0.06170.01270.06320.00330.10140.0026-0.01160.00640.00220.0011-0.0201-0.01350.0209-0.00370.0083-0.00370.00140.0101-0.00230.027918.951351.153514.1529
30.2475-0.1076-0.04580.28690.01060.47010.0087-0.006-0.00870.0073-0.00220.0236-0.0006-0.0309-0.00650.0022-0.00080.00230.00260.00090.0227-5.212760.836528.3671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 243
2X-RAY DIFFRACTION2B1 - 243
3X-RAY DIFFRACTION3C1 - 243

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