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- PDB-4di0: The structure of Rubrerythrin from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 4di0
TitleThe structure of Rubrerythrin from Burkholderia pseudomallei
ComponentsRubrerythrin
KeywordsOXIDOREDUCTASE / SSGCID / seattle structural genomics center for infectious disease / peroxidase
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
: / Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: The structure of Rubrerythrin from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Rubrerythrin
B: Rubrerythrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,93210
Polymers31,4242
Non-polymers5088
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-65 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.580, 56.470, 99.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rubrerythrin


Mass: 15712.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_A0924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JK21
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: BupsA.17633.a at 29.52 mg/ml, 16% PEG8000, 20% glycerol, 40mM potassium phosphate. Additional ethylene glycol as cryoprotectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22862 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.573 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 29.81
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.950.5463.7598861618195.3
1.95-20.4244.7599761567197.2
2-2.060.2846.94102311564198.5
2.06-2.120.2189.28105831529199.5
2.12-2.190.15814.03122961496199.8
2.19-2.270.13217.57132501464199.8
2.27-2.360.1219.03130681395199.9
2.36-2.450.10721.36132791359199.8
2.45-2.560.09624.3134351289199.6
2.56-2.690.07729.551380312451100
2.69-2.830.06935.01149721201199.8
2.83-30.06440.171572311131100
3-3.210.05643.361496410561100
3.21-3.470.04254.271408210001100
3.47-3.80.03567.1812918925199.9
3.8-4.250.0375.73115638371100
4.25-4.910.02877.95102587441100
4.91-6.010.03365.528753640199.8
6.01-8.50.02971.3668015191100
8.5-500.02977.163449301198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å45.05 Å
Translation2.5 Å45.05 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J30

1j30


Resolution: 1.9→37.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1862 / WRfactor Rwork: 0.1578 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.89 / SU B: 4.911 / SU ML: 0.075 / SU R Cruickshank DPI: 0.145 / SU Rfree: 0.1281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 1180 5.2 %RANDOM
Rwork0.1692 ---
obs0.1707 22862 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.16 Å2 / Biso mean: 21.007 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 25 187 2353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022232
X-RAY DIFFRACTIONr_bond_other_d0.0020.021485
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.943017
X-RAY DIFFRACTIONr_angle_other_deg0.94533596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7285289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02724.359117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55315344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0011514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02481
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 87 -
Rwork0.228 1407 -
all-1494 -
obs--94.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.85270.4771-1.00250.8878-0.27781.2317-0.00340.04640.01090.0393-0.0059-0.0621-0.0105-0.02890.00930.06880.016-0.01340.0480.00460.084545.313756.55989.7667
20.7306-0.764-0.08092.75730.48931.804-0.048-0.0383-0.07860.13160.05790.12150.0749-0.1552-0.00990.1079-0.00490.00380.05860.01240.079745.842739.931521.4364
30.5783-0.03761.11341.1520.80924.9548-0.02590.0338-0.0620.0964-0.009-0.02780.1673-0.02670.03490.07620.0090.00940.0729-0.02150.092452.257433.54212.0095
45.3618-0.60161.47055.5106-0.520912.9643-0.0561-0.01590.07270.15240.1203-0.1935-0.30020.1915-0.06420.08760.0119-0.03610.01480.00840.0856.665237.619926.674
50.6525-0.10230.61861.00610.71963.42840.00020.05880.01410.0746-0.0046-0.0717-0.00140.04120.00440.06160.0039-0.0070.04090.00470.094951.254146.072510.67
61.7174-0.7770.32431.46080.59511.01690.04440.24440.0038-0.1643-0.04450.0005-0.0137-0.09060.00010.1001-0.00320.01920.12160.01550.088645.796757.6573-5.2743
73.01141.5499-1.98622.1505-1.49643.0307-0.01770.07960.08540.05780.00690.0645-0.0827-0.18280.01080.05490.042-0.01580.0685-0.01420.066732.623562.403612.2907
83.83881.1302-2.88141.98630.944.16850.15560.01080.2594-0.07840.05550.0301-0.3436-0.0313-0.21110.1760.0864-0.0150.12250.04020.146348.471670.5864-3.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 65
2X-RAY DIFFRACTION2A66 - 95
3X-RAY DIFFRACTION3A96 - 127
4X-RAY DIFFRACTION4A128 - 140
5X-RAY DIFFRACTION5B2 - 64
6X-RAY DIFFRACTION6B65 - 91
7X-RAY DIFFRACTION7B92 - 129
8X-RAY DIFFRACTION8B130 - 139

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