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- PDB-5nw3: The cryofrozen atomic resolution X-ray crystal structure of perde... -

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Basic information

Entry
Database: PDB / ID: 5nw3
TitleThe cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution)
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / Perdeuterated rubredoxin / pyrococcus furiosus / atomic resolution
Function / homology
Function and homology information


electron transfer activity / iron ion binding
Similarity search - Function
Rubredoxin / Rubredoxin, iron-binding site / Rubredoxin signature. / Rubrerythrin, domain 2 - #10 / Rubredoxin domain / Rubredoxin / Rubredoxin-like domain / Rubredoxin-like domain profile. / Rubrerythrin, domain 2 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
: / : / PHOSPHATE ION / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.59 Å
AuthorsCuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Forsyth, V.T.
Funding support United Kingdom, France, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
ILL France
CitationJournal: To Be Published
Title: The cryofrozen atomic resolution X-ray crystal structure of perdeuterated Pyrococcus furiosus Rubredoxin (100K, 0.59A resolution)
Authors: Cuypers, M.G. / Mason, S.A. / Mossou, E. / Haertlein, M. / Forsyth, V.T.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,2455
Polymers6,0321
Non-polymers2134
Water3,315184
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-9 kcal/mol
Surface area3540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.622, 34.533, 43.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Rubredoxin / / Rd


Mass: 6031.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: rub, PF1282
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P24297

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Non-polymers , 5 types, 188 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: seeded 3.4M equimolar Na/K phosphate buffer / Temp details: controlled room t.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.61992 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.61992 Å / Relative weight: 1
ReflectionResolution: 0.59→43.07 Å / Num. obs: 115950 / % possible obs: 85.6 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 17.7
Reflection shellResolution: 0.59→0.6 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5865 / CC1/2: 0.563 / Rpim(I) all: 0.369 / Rrim(I) all: 0.578 / % possible all: 30.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
XDSdata reduction
SCALAdata scaling
ACORNphasing
RefinementResolution: 0.59→21.535 Å / SU ML: 0.03 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.23
RfactorNum. reflection% reflection
Rfree0.1458 5830 5.03 %
Rwork0.1345 --
obs0.1351 115859 85.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.59→21.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 8 184 613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006463
X-RAY DIFFRACTIONf_angle_d0.99634
X-RAY DIFFRACTIONf_dihedral_angle_d12.409174
X-RAY DIFFRACTIONf_chiral_restr0.08461
X-RAY DIFFRACTIONf_plane_restr0.00987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.5851-0.59170.1937160.3088244X-RAY DIFFRACTION6
0.5917-0.59870.2538430.2627919X-RAY DIFFRACTION22
0.5987-0.6060.2835730.26081472X-RAY DIFFRACTION35
0.606-0.61370.23331020.23762060X-RAY DIFFRACTION48
0.6137-0.62170.2091310.22012469X-RAY DIFFRACTION58
0.6217-0.63030.22651560.20962789X-RAY DIFFRACTION66
0.6303-0.63930.20341850.21043118X-RAY DIFFRACTION74
0.6393-0.64880.18911790.18973447X-RAY DIFFRACTION81
0.6488-0.6590.17031940.18393672X-RAY DIFFRACTION86
0.659-0.66980.16712150.16923923X-RAY DIFFRACTION93
0.6698-0.68130.16942240.16034230X-RAY DIFFRACTION99
0.6813-0.69370.15312210.15614218X-RAY DIFFRACTION99
0.6937-0.7070.16842260.15174257X-RAY DIFFRACTION100
0.707-0.72150.14652380.14924206X-RAY DIFFRACTION100
0.7215-0.73720.14982400.14664235X-RAY DIFFRACTION100
0.7372-0.75430.13262100.14164282X-RAY DIFFRACTION100
0.7543-0.77320.14742210.14114232X-RAY DIFFRACTION100
0.7732-0.79410.16382290.14214286X-RAY DIFFRACTION100
0.7941-0.81740.1512120.13924300X-RAY DIFFRACTION100
0.8174-0.84380.12912310.14014268X-RAY DIFFRACTION100
0.8438-0.8740.12962250.13164274X-RAY DIFFRACTION100
0.874-0.9090.14031890.12484350X-RAY DIFFRACTION100
0.909-0.95040.13222210.12224265X-RAY DIFFRACTION100
0.9504-1.00050.11112050.12074321X-RAY DIFFRACTION100
1.0005-1.06310.11392480.11694280X-RAY DIFFRACTION100
1.0631-1.14520.10862260.11294337X-RAY DIFFRACTION100
1.1452-1.26050.132420.1164318X-RAY DIFFRACTION100
1.2605-1.44280.13522340.12324330X-RAY DIFFRACTION99
1.4428-1.81770.15462380.12664388X-RAY DIFFRACTION100
1.8177-21.55010.16132560.13364539X-RAY DIFFRACTION99

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