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- PDB-2fdr: Crystal Structure of Conserved Haloacid Dehalogenase-like Protein... -

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Basic information

Entry
Database: PDB / ID: 2fdr
TitleCrystal Structure of Conserved Haloacid Dehalogenase-like Protein of Unknown Function ATU0790 from Agrobacterium tumefaciens str. C58
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical / SAD / Agrobacterium tumefaciens / HAD-superfamily hydrolase / putative b-phosphoglucomutase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Haloacid dehalogenase-like hydrolase / : / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Haloacid dehalogenase-like hydrolase / : / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / 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
: / HAD family hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsNocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of hydrolases/phosphatases-like fold protein from Agrobacterium tumefaciens str. C58
Authors: Nocek, B. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 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
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3571
Non-polymers241
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.237, 48.179, 104.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein conserved hypothetical protein


Mass: 25356.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Plasmid: peT15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 17739162, UniProt: A9CJW3*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 1.99 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M Tris ph7.8, 0.5M Sodium Acetate, 24% PEG4K, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 6, 2005 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→52.2 Å / Num. obs: 13606 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26.2
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.1 / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
SOLVEphasing
RESOLVEphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
CCP4phasing
SHELXEmodel building
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→52.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.826 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 688 5.1 %RANDOM
Rwork0.174 ---
obs0.177 12918 95.5 %-
all-13606 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å20 Å20 Å2
2---0.95 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 1 139 1828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221769
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9742393
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.31322.95871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.20315311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6131515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021319
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.2864
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21231
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.51161
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24721828
X-RAY DIFFRACTIONr_scbond_it2.2493666
X-RAY DIFFRACTIONr_scangle_it3.424.5565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 53 -
Rwork0.199 866 -
obs--90.99 %
Refinement TLS params.Method: refined / Origin x: 29.2042 Å / Origin y: 22.7885 Å / Origin z: 10.1972 Å
111213212223313233
T-0.0258 Å20.0031 Å20.0052 Å2--0.0117 Å20.0034 Å2---0.0004 Å2
L0.5494 °2-0.0019 °20.3165 °2-0.3617 °20.1916 °2--0.3563 °2
S-0.0375 Å °-0.028 Å °-0.0478 Å °0.0342 Å °0.0309 Å °-0.0098 Å °0.0107 Å °-0.0313 Å °0.0066 Å °

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