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- PDB-2r6u: Crystal structure of gene product RHA04853 from Rhodococcus sp. RHA1 -

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Basic information

Entry
Database: PDB / ID: 2r6u
TitleCrystal structure of gene product RHA04853 from Rhodococcus sp. RHA1
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / RHA04853 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / Bleomycin resistance protein-like N-terminal / : / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
VOC domain-containing protein
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of gene product RHA04853 from Rhodococcus sp. RHA1.
Authors: Zhang, R. / Xu, X. / Gu, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)64,4674
Polymers64,4674
Non-polymers00
Water12,016667
1
A: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,2342
Polymers32,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,2342
Polymers32,2342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.411, 89.048, 58.913
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThis protein existed as dimer. There are two dimers in the asymmtric unit: Mol.A/Mol.C, Mol.B/Mol.D

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Components

#1: Protein
Uncharacterized protein


Mass: 16116.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA04853, RHA1_ro04536 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0S814
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 2.09 Å3/Da / Density % sol: 41.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Na(OAC), 0.2M Ammonium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Oct 8, 2006 / 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: 1.5→58.72 Å / Num. all: 80327 / Num. obs: 79299 / % possible obs: 98.72 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 32.3
Reflection shellResolution: 1.5→1.538 Å / Redundancy: 7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.85 / Num. unique all: 5882 / % possible all: 88.54

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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: 1.5→58.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.327 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.077
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21076 4173 5 %RANDOM
Rwork0.17614 ---
all0.17786 79299 --
obs0.17786 79299 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å2-0.01 Å2
2---0.3 Å20 Å2
3---0.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.043 Å0.035 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.5→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3875 0 0 667 4542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223978
X-RAY DIFFRACTIONr_bond_other_d0.0020.022654
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9485398
X-RAY DIFFRACTIONr_angle_other_deg0.9136414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4045508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3923.69187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32315600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.291531
X-RAY DIFFRACTIONr_chiral_restr0.1780.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024569
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_nbd_refined0.2310.2868
X-RAY DIFFRACTIONr_nbd_other0.220.22924
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21986
X-RAY DIFFRACTIONr_nbtor_other0.0870.22183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2517
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.235
X-RAY DIFFRACTIONr_mcbond_it1.4581.53218
X-RAY DIFFRACTIONr_mcbond_other0.2371.51063
X-RAY DIFFRACTIONr_mcangle_it1.51824039
X-RAY DIFFRACTIONr_scbond_it2.56731716
X-RAY DIFFRACTIONr_scangle_it3.4874.51359
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 276 -
Rwork0.217 5208 -
obs-5484 88.54 %
Refinement TLS params.Method: refined / Origin x: -10.877 Å / Origin y: 34.26 Å / Origin z: 45.823 Å
111213212223313233
T-0.0593 Å20.0034 Å2-0.0147 Å2--0.0632 Å20.0084 Å2---0.0303 Å2
L0.9814 °20.0082 °2-0.1704 °2-0.3909 °20.0899 °2--0.4409 °2
S-0.0394 Å °-0.0019 Å °-0.0538 Å °-0.0095 Å °0.007 Å °0.0394 Å °0.0011 Å °-0.0167 Å °0.0325 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 5517 - 76
2X-RAY DIFFRACTION1AA56 - 12577 - 146
3X-RAY DIFFRACTION1BB1 - 5522 - 76
4X-RAY DIFFRACTION1BB56 - 12577 - 146
5X-RAY DIFFRACTION1CC-1 - 5520 - 76
6X-RAY DIFFRACTION1CC56 - 12477 - 145
7X-RAY DIFFRACTION1DD-5 - 5516 - 76
8X-RAY DIFFRACTION1DD56 - 12577 - 146

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