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- PDB-3kyu: X-ray crystal structure determination of fully perdeuterated rubr... -

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Basic information

Entry
Database: PDB / ID: 3kyu
TitleX-ray crystal structure determination of fully perdeuterated rubredoxin at 100K
ComponentsRubredoxin
KeywordsELECTRON TRANSPORT / Iron / Metal-binding / Transport
Function / homology
Function and homology information


alkane catabolic process / 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 ...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
DEUTERATED WATER / : / Rubredoxin
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsGardberg, A.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.
Authors: Gardberg, A.S. / Del Castillo, A.R. / Weiss, K.L. / Meilleur, F. / Blakeley, M.P. / Myles, D.A.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0321
Non-polymers561
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.889, 34.632, 43.255
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 Rubredoxin / Rd


Mass: 6031.728 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ab-initio perdeuteration / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rub, PF1282 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P24297
#2: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: D2O

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growMethod: hanging drop / Details: 3.8 M sodium/potassium phosphate, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR225 / Detector: CCD / Date: Mar 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→27.04 Å / Num. obs: 21196

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
ELVESdata reduction
ELVESdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BRF

1brf


Resolution: 1.1→27.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 0.483 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12485 1076 5.1 %RANDOM
Rwork0.10645 ---
obs0.10736 20120 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.1→27.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms421 0 1 137 559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022481
X-RAY DIFFRACTIONr_bond_other_d0.0030.02336
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.996661
X-RAY DIFFRACTIONr_angle_other_deg0.9113836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.021563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55827.14321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.3751580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.263
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0284
X-RAY DIFFRACTIONr_nbd_refined0.2510.2102
X-RAY DIFFRACTIONr_nbd_other0.1830.2356
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2244
X-RAY DIFFRACTIONr_nbtor_other0.090.2218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2101
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0325389
X-RAY DIFFRACTIONr_mcbond_other1.0975115
X-RAY DIFFRACTIONr_mcangle_it2.2963496
X-RAY DIFFRACTIONr_scbond_it2.52218
X-RAY DIFFRACTIONr_scangle_it3.5043165
X-RAY DIFFRACTIONr_rigid_bond_restr1.5173607
X-RAY DIFFRACTIONr_sphericity_free8.161393
X-RAY DIFFRACTIONr_sphericity_bonded3.4653462
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.134 76 -
Rwork0.117 1396 -
obs--95.58 %

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