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- PDB-2i6x: The structure of a predicted HAD-like family hydrolase from Porph... -

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Basic information

Entry
Database: PDB / ID: 2i6x
TitleThe structure of a predicted HAD-like family hydrolase from Porphyromonas gingivalis.
ComponentsHydrolase, haloacid dehalogenase-like family
KeywordsHYDROLASE / Porphyromonas gingivalis / HAD superfamily / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Hydrolase, haloacid dehalogenase-like family
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsCuff, M.E. / Mussar, K.E. / Li, H. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a predicted HAD-like family hydrolase from Porphyromonas gingivalis. (CASP Target)
Authors: Cuff, M.E. / Mussar, K.E. / Li, H. / Moy, S. / Joachimiak, A.
History
DepositionAug 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrolase, haloacid dehalogenase-like family


Theoretical massNumber of molelcules
Total (without water)24,6111
Polymers24,6111
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.727, 78.727, 139.879
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Hydrolase, haloacid dehalogenase-like family /


Mass: 24610.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0725 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): TIGR4 / References: UniProt: Q7MWA6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M K/Na tartrate, 0.1M Tris pH7.0, 0.2M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979616, 0.97951
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796161
20.979511
ReflectionResolution: 2.4→38.8 Å / Num. all: 10573 / Num. obs: 10573 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.46 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.4→38.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 16.427 / SU ML: 0.207 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.424 / ESU R Free: 0.289
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27583 505 4.8 %RANDOM
Rwork0.20948 ---
all0.21271 1573 --
obs0.21271 10067 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.905 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.84 Å20 Å2
2--1.68 Å20 Å2
3----2.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 110 1769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221779
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9812411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.86323.61794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9881517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021392
X-RAY DIFFRACTIONr_nbd_refined0.2110.2816
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.216
X-RAY DIFFRACTIONr_mcbond_it0.9121.51102
X-RAY DIFFRACTIONr_mcangle_it1.1721726
X-RAY DIFFRACTIONr_scbond_it2.1933762
X-RAY DIFFRACTIONr_scangle_it3.2574.5682
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 35 -
Rwork0.227 719 -
obs--98.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.52882.48411.65774.77150.35472.18030.0310.40580.351-0.1121-0.10690.1213-0.34750.21110.0759-0.3846-0.05090.01390.0182-0.0019-0.235956.084617.05422.7369
29.5120.4586-1.27143.49141.23878.49690.3033-0.1463-0.6020.5795-0.17280.09691.4191-0.9975-0.13050.0262-0.3396-0.08610.03340.011-0.229559.22627.498224.9772
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 154 - 18
2X-RAY DIFFRACTION1AA85 - 20788 - 210
3X-RAY DIFFRACTION2AA16 - 8419 - 87

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