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- PDB-3brc: Crystal structure of a conserved protein of unknown function from... -

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Basic information

Entry
Database: PDB / ID: 3brc
TitleCrystal structure of a conserved protein of unknown function from Methanobacterium thermoautotrophicum
ComponentsConserved protein of unknown function
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved protein / Methanobacterium thermoautotrophicum / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / Helix hairpin bin / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Conserved protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsZhang, R. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved protein of unknown function from Methanobacterium thermoautotrophicum.
Authors: Zhang, R. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein of unknown function
B: Conserved protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0725
Polymers35,7872
Non-polymers2853
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
MethodPISA
2
A: Conserved protein of unknown function
B: Conserved protein of unknown function
hetero molecules

A: Conserved protein of unknown function
B: Conserved protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,14410
Polymers71,5744
Non-polymers5706
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.894, 48.916, 63.868
Angle α, β, γ (deg.)90.00, 118.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-212-

HOH

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Components

#1: Protein Conserved protein of unknown function


Mass: 17893.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH1144, GI:2622249 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O27213
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Ammonium phosphate, 16% PEG 3350, 2% Glycerol, 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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→88.52 Å / Num. all: 36473 / Num. obs: 32286 / % possible obs: 88.52 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 27.05
Reflection shellResolution: 1.6→1.642 Å / Redundancy: 2 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 1.35 / Num. unique all: 2852 / % possible all: 40.92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→56.08 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.177 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.178 / ESU R Free: 0.116
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23669 1703 5 %RANDOM
Rwork0.18324 ---
all0.18586 32286 --
obs0.18586 32286 88.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.697 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å21.07 Å2
2---0.95 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.6→56.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 15 226 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212483
X-RAY DIFFRACTIONr_bond_other_d0.0020.021759
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9713346
X-RAY DIFFRACTIONr_angle_other_deg0.92434227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0535308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66821.795117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7621537
X-RAY DIFFRACTIONr_chiral_restr0.0750.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
X-RAY DIFFRACTIONr_nbd_refined0.2460.2584
X-RAY DIFFRACTIONr_nbd_other0.220.21954
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21188
X-RAY DIFFRACTIONr_nbtor_other0.0830.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.250
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.210
X-RAY DIFFRACTIONr_mcbond_it1.9491.51904
X-RAY DIFFRACTIONr_mcbond_other0.551.5626
X-RAY DIFFRACTIONr_mcangle_it1.93222468
X-RAY DIFFRACTIONr_scbond_it3.58231021
X-RAY DIFFRACTIONr_scangle_it4.734.5878
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 58 -
Rwork0.223 1109 -
obs-1167 40.92 %
Refinement TLS params.Method: refined / Origin x: 6.0672 Å / Origin y: 1.8108 Å / Origin z: 12.2825 Å
111213212223313233
T-0.0328 Å20.0104 Å2-0.0123 Å2--0.038 Å2-0.0073 Å2---0.0458 Å2
L0.8782 °20.0415 °2-0.3779 °2-0.87 °2-0.0214 °2--0.8725 °2
S-0.0347 Å °-0.0544 Å °0.0219 Å °0.1405 Å °0.0162 Å °-0.0359 Å °0.0271 Å °0.0851 Å °0.0184 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 501 - 50
2X-RAY DIFFRACTION1AA51 - 10051 - 100
3X-RAY DIFFRACTION1AA101 - 155101 - 155
4X-RAY DIFFRACTION1BB2 - 502 - 50
5X-RAY DIFFRACTION1BB51 - 10051 - 100
6X-RAY DIFFRACTION1BB101 - 156101 - 156

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