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- PDB-3qgm: p-nitrophenyl phosphatase from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 3qgm
Titlep-nitrophenyl phosphatase from Archaeoglobus fulgidus
Componentsp-nitrophenyl phosphatase (Pho2)
KeywordsHYDROLASE / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
p-nitrophenyl phosphatase (Pho2)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsOsipiuk, J. / Zheng, H. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: p-nitrophenyl phosphatase from Archaeoglobus fulgidus.
Authors: Osipiuk, J. / Zheng, H. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p-nitrophenyl phosphatase (Pho2)
B: p-nitrophenyl phosphatase (Pho2)
C: p-nitrophenyl phosphatase (Pho2)
D: p-nitrophenyl phosphatase (Pho2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2639
Polymers119,0404
Non-polymers2225
Water8,125451
1
A: p-nitrophenyl phosphatase (Pho2)
B: p-nitrophenyl phosphatase (Pho2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6625
Polymers59,5202
Non-polymers1423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-43 kcal/mol
Surface area21380 Å2
MethodPISA
2
C: p-nitrophenyl phosphatase (Pho2)
D: p-nitrophenyl phosphatase (Pho2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6004
Polymers59,5202
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-47 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.252, 68.843, 70.154
Angle α, β, γ (deg.)74.990, 87.330, 85.760
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
p-nitrophenyl phosphatase (Pho2)


Mass: 29760.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_0374 / Plasmid: pET15b modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O29873
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris buffer, 0.2 M calcium chloride, 26% PEG-3350, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2006
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→37.2 Å / Num. all: 62618 / Num. obs: 62618 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.09 / Χ2: 3.233 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.032.80.5221.9920461.16362.7
2.03-2.073.10.4325191.1475.1
2.07-2.113.30.37531021.18194.1
2.11-2.153.70.33131461.25596.6
2.15-2.23.80.27931951.26997.3
2.2-2.253.90.25732161.34496.9
2.25-2.313.90.22332061.36898.1
2.31-2.373.90.18931981.51497.2
2.37-2.443.90.16732401.5698.3
2.44-2.523.90.15532241.6898
2.52-2.613.90.1432141.88797.9
2.61-2.713.90.12332612.12497.8
2.71-2.843.90.10932342.48998.7
2.84-2.993.90.09432562.77598.6
2.99-3.173.90.08332463.27198.6
3.17-3.423.90.07732444.09498.8
3.42-3.763.90.06832634.77999.2
3.76-4.313.90.0732686.2799.1
4.31-5.433.80.0732828.38399.4
5.43-503.90.074325812.37999

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→37.2 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 8.903 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.211 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 3161 5 %RANDOM
Rwork0.1692 ---
all0.1715 62618 --
obs0.1715 62618 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 69.85 Å2 / Biso mean: 33.606 Å2 / Biso min: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20.2 Å20.09 Å2
2---0.37 Å20.65 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8060 0 8 451 8519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0228489
X-RAY DIFFRACTIONr_bond_other_d0.0020.025967
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.99811523
X-RAY DIFFRACTIONr_angle_other_deg0.929314637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11951131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.06624.038369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.047151622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.641578
X-RAY DIFFRACTIONr_chiral_restr0.0960.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021638
X-RAY DIFFRACTIONr_mcbond_it0.8881.55308
X-RAY DIFFRACTIONr_mcbond_other0.2391.52196
X-RAY DIFFRACTIONr_mcangle_it1.56428637
X-RAY DIFFRACTIONr_scbond_it2.54733181
X-RAY DIFFRACTIONr_scangle_it4.1584.52842
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 127 -
Rwork0.244 3028 -
all-3155 -
obs-3155 65.06 %
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)
11.0827-0.25220.09160.4039-0.20950.29-0.0866-0.04620.08550.0140.0366-0.0347-0.07210.04140.05010.1260.0238-0.00250.04340.01380.0286-0.825431.82840.4089
21.07050.09810.26370.7580.04350.9434-0.0298-0.00550.0472-0.0540.0230.07540.0513-0.08190.00680.0514-0.0198-0.00360.03040.02370.0385-22.694837.9366-34.0169
31.8754-0.1059-0.40970.43180.11640.8204-0.07860.0291-0.1620.00110.0224-0.03880.0571-0.03090.05620.04540.0150.00430.02020.00020.03-1.1518-0.2713-0.1305
41.4153-0.1821-0.69770.06490.20810.84440.05730.13380.0773-0.0597-0.03310.0107-0.15-0.1419-0.02430.1185-0.01550.01840.0809-0.00590.086620.62255.0938-34.4663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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