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- PDB-2hzb: X-Ray Crystal Structure of Protein BH3568 from Bacillus haloduran... -

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Basic information

Entry
Database: PDB / ID: 2hzb
TitleX-Ray Crystal Structure of Protein BH3568 from Bacillus halodurans. Northeast Structural Genomics Consortium BhR60.
ComponentsHypothetical UPF0052 protein BH3568
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / BhR60 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


LPPG:FO 2-phospho-L-lactate transferase activity / regulation of cell shape / cytoplasm
Similarity search - Function
Gluconeogenesis factor / CofD-like domains / 2-phospho-L-lactate transferase CofD / CofD-like domain superfamily / 2-phospho-L-lactate transferase CofD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Gluconeogenesis factor
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the hypothetical UPF0052 protein BH3568 from Bacillus halodurans. Northeast Structural Genomics Consortium BhR60.
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Benach, J. / Shastry, R. / Conover, K. / Ma, L.C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0052 protein BH3568
B: Hypothetical UPF0052 protein BH3568
C: Hypothetical UPF0052 protein BH3568
D: Hypothetical UPF0052 protein BH3568


Theoretical massNumber of molelcules
Total (without water)144,1904
Polymers144,1904
Non-polymers00
Water2,432135
1
A: Hypothetical UPF0052 protein BH3568
B: Hypothetical UPF0052 protein BH3568


Theoretical massNumber of molelcules
Total (without water)72,0952
Polymers72,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-24 kcal/mol
Surface area25630 Å2
MethodPISA
2
C: Hypothetical UPF0052 protein BH3568
D: Hypothetical UPF0052 protein BH3568


Theoretical massNumber of molelcules
Total (without water)72,0952
Polymers72,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-23 kcal/mol
Surface area25710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.725, 142.012, 229.562
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
Hypothetical UPF0052 protein BH3568


Mass: 36047.461 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH3568 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9K706
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.92 Å3/Da / Density % sol: 57.91 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / pH: 7
Details: 2.4M Sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9793, 0.9796, 0.9681
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2006 / Details: MIRRORS
RadiationMonochromator: SI 111 CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97961
30.96811
ReflectionResolution: 2.8→30 Å / Num. all: 79533 / Num. obs: 71260 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 44670.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3395 4.8 %RANDOM
Rwork0.185 ---
obs0.185 71260 88.8 %-
all-75971 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.48 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--2.24 Å20 Å2
3----1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9340 0 0 135 9475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 335 3.5 %
Rwork0.261 9184 -
obs--71.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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