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- PDB-4jgb: Crystal Structure of Putative exported protein from Burkholderia ... -

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Basic information

Entry
Database: PDB / ID: 4jgb
TitleCrystal Structure of Putative exported protein from Burkholderia pseudomallei
ComponentsPutative exported protein
KeywordsPROTEIN BINDING / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Putative exported protein
Function / homologyNAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative exported protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Putative exported protein from Burkholderia pseudomallei
Authors: Dranow, D.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionFeb 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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 / _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

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Assembly

Deposited unit
A: Putative exported protein
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3927
Polymers43,9462
Non-polymers4465
Water4,306239
1
A: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2274
Polymers21,9731
Non-polymers2543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1653
Polymers21,9731
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.390, 76.280, 78.580
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative exported protein


Mass: 21972.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSL1273 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63VH2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: JCSG+, D4: 0.2M Lithium sulfate, 0.1M Sodium acetate pH 4.5, 30% (w/v) PEG8000, 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: Sep 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 25023 / Num. obs: 24798 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.859 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.10.2883.794279170792.5
2.1-2.160.2844.795487175598.9
2.16-2.220.2456.136361175699.7
2.22-2.290.2226.636165168999.6
2.29-2.370.1937.415976163399.8
2.37-2.450.1648.275917160399.9
2.45-2.540.1628.357911557100
2.54-2.650.1459.265394145299.6
2.65-2.760.12210.475228139699.8
2.76-2.90.09912.5450761362100
2.9-3.060.0814.254868129699.5
3.06-3.240.0731645361208100
3.24-3.470.05619.4343431156100
3.47-3.740.04424.494012106999.7
3.74-4.10.0427.45368398099.7
4.1-4.580.04427.76340791299.6
4.58-5.290.04724.72289878199.4
5.29-6.480.06218.98251367299.4
6.48-9.170.04427.13192752499.4
9.170.03233.0399429096.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHN

3dhn


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.761 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 1264 5.1 %RANDOM
Rwork0.2039 ---
obs0.2069 24798 99.1 %-
all-25023 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.68 Å2 / Biso mean: 20.928 Å2 / Biso min: 5.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å2-0 Å20.05 Å2
2---0.87 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 24 239 3226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193050
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9574148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8135413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89523.36125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54615437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9581524
X-RAY DIFFRACTIONr_chiral_restr0.0910.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212348
X-RAY DIFFRACTIONr_mcbond_it0.6641.1851646
X-RAY DIFFRACTIONr_mcangle_it1.1161.7712052
X-RAY DIFFRACTIONr_scbond_it1.0141.2931404
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 79 -
Rwork0.217 1625 -
all-1704 -
obs--92.16 %
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)
12.67250.2305-0.69111.7862-0.03712.4905-0.14960.1097-0.16670.15930.00690.2228-0.0387-0.2630.14270.05350.00090.03140.0287-0.01410.071810.738121.61638.3601
21.17670.2647-0.15341.7524-0.2080.86620.01720.01670.07190.08140.0319-0.0198-0.0545-0.0197-0.04910.02970.01320.01710.02290.0060.017819.749135.85110.1829
31.1680.93950.14622.82961.76083.5774-0.221-0.07850.1929-0.3201-0.14130.5308-0.2201-0.38060.36230.07030.0379-0.09450.0538-0.0440.168742.828238.979631.1761
41.16560.10880.53532.52680.48560.6492-0.0155-0.0123-0.0037-0.3391-0.0130.0567-0.0117-0.00080.02850.0681-0.0023-0.01010.0121-0.0010.006250.93524.382429.2829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A76 - 209
3X-RAY DIFFRACTION3B1 - 74
4X-RAY DIFFRACTION4B75 - 209

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