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- PDB-2pn0: Prokaryotic transcription elongation factor GreA/GreB from Nitros... -

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Basic information

Entry
Database: PDB / ID: 2pn0
TitleProkaryotic transcription elongation factor GreA/GreB from Nitrosomonas europaea
ComponentsProkaryotic transcription elongation factor GreA/GreB
KeywordsTRANSCRIPTION / Transcription elongation factor / GreA/GreB / structural genomics / APC6349 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-templated transcription elongation / RNA polymerase binding / translation elongation factor activity / regulation of DNA-templated transcription elongation / DNA binding
Similarity search - Function
Regulator of nucleoside diphosphate kinase, N-terminal domain / Rnk N-terminus / GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / GTP Cyclohydrolase I; Chain A, domain 1 / Chitinase A; domain 3 ...Regulator of nucleoside diphosphate kinase, N-terminal domain / Rnk N-terminus / GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Transcription elongation factor, GreA/GreB, C-terminal domain / Transcription elongation factor, GreA/GreB, C-terminal / Transcription elongation factor GreA/GreB family / Transcription elongation factor, GreA/GreB, C-term / Transcription elongation factor GreA/GreB, C-terminal domain superfamily / GTP Cyclohydrolase I; Chain A, domain 1 / Chitinase A; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Prokaryotic transcription elongation factor GreA/GreB
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsOsipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of prokaryotic transcription elongation factor GreA/GreB from Nitrosomonas europaea.
Authors: Osipiuk, J. / Evdokimova, E. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prokaryotic transcription elongation factor GreA/GreB
B: Prokaryotic transcription elongation factor GreA/GreB
C: Prokaryotic transcription elongation factor GreA/GreB
D: Prokaryotic transcription elongation factor GreA/GreB


Theoretical massNumber of molelcules
Total (without water)62,7134
Polymers62,7134
Non-polymers00
Water10,215567
1
A: Prokaryotic transcription elongation factor GreA/GreB
D: Prokaryotic transcription elongation factor GreA/GreB


Theoretical massNumber of molelcules
Total (without water)31,3562
Polymers31,3562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-23 kcal/mol
Surface area12090 Å2
MethodPISA
2
B: Prokaryotic transcription elongation factor GreA/GreB
C: Prokaryotic transcription elongation factor GreA/GreB


Theoretical massNumber of molelcules
Total (without water)31,3562
Polymers31,3562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.628, 80.838, 171.387
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsunknown, putative dimer

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Components

#1: Protein
Prokaryotic transcription elongation factor GreA/GreB


Mass: 15678.198 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: IFO 14298 / Gene: rnk, NE2130 / Plasmid: pET15b modified / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q82T10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.05 M Calcium chloride, 0.1 M Na Acetate, 20% PEG3350, pH 4.6, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 18, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.7→39.9 Å / Num. all: 58450 / Num. obs: 58450 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 37.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 1.76 / Num. unique all: 3521 / % possible all: 90.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→39.9 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.823 / SU ML: 0.068 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 2950 5.1 %RANDOM
Rwork0.1766 ---
all0.1781 55435 --
obs0.1781 55435 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.619 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2--0.27 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 0 571 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.582.0135607
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31924.831178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17915752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2541534
X-RAY DIFFRACTIONr_chiral_restr0.1170.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023070
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.22113
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22874
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2453
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.297
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0491.52659
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50824226
X-RAY DIFFRACTIONr_scbond_it2.39531578
X-RAY DIFFRACTIONr_scangle_it3.7564.51344
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 209 -
Rwork0.285 3680 -
obs-3889 90.23 %

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