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- PDB-3slg: Crystal structure of PbgP3 protein from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 3slg
TitleCrystal structure of PbgP3 protein from Burkholderia pseudomallei
ComponentsPbgP3 protein
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / melioidosis / glanders / NAD-dependent epimerase/dehydratase family protein
Function / homology
Function and homology information


carboxy-lyase activity
Similarity search - Function
Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / : / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / : / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of PbgP3 protein from Burkholderia pseudomallei
Authors: Edwards, T.E. / Abendroth, J. / Sankaran, B. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJun 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / 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

Downloads & links

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Assembly

Deposited unit
A: PbgP3 protein
B: PbgP3 protein
C: PbgP3 protein
D: PbgP3 protein
E: PbgP3 protein
F: PbgP3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,15318
Polymers251,7286
Non-polymers42512
Water15,871881
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-216 kcal/mol
Surface area70360 Å2
MethodPISA
2
A: PbgP3 protein
F: PbgP3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0516
Polymers83,9092
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-68 kcal/mol
Surface area25120 Å2
MethodPISA
3
B: PbgP3 protein
C: PbgP3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0516
Polymers83,9092
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-67 kcal/mol
Surface area25220 Å2
MethodPISA
4
D: PbgP3 protein
E: PbgP3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0516
Polymers83,9092
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-66 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.570, 91.550, 147.260
Angle α, β, γ (deg.)90.000, 91.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PbgP3 protein


Mass: 41954.629 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_2404 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JRK4
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 881 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein at 8.2 mg/mL against PACT screen condition C10, 20% PEG 6000, 0.2 M MgCl2, 0.1 M Hepes, 20% ethylene glycol as cryo-protection reagent, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 129532 / Num. obs: 128239 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 34.447 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.1-2.152.80.4282.23261399518946199.4
2.15-2.210.3582.7125612926299.2
2.21-2.280.2943.2524696892499.3
2.28-2.350.2513.8324254876199.3
2.35-2.420.2124.5623412845599.5
2.42-2.510.1725.5322636816699.2
2.51-2.60.1526.3921880789399.3
2.6-2.710.1257.6321156761399.3
2.71-2.830.0979.8320231729699.2
2.83-2.970.08311.5619356697899.2
2.97-3.130.06614.2418432664099.2
3.13-3.320.04719.0817288623898.9
3.32-3.550.03524.9916451592898.9
3.55-3.830.02930.4615073547298.7
3.83-4.20.02435.9113780502998.1
4.2-4.70.02239.6212439455798.3
4.7-5.420.02239.9110756401097.6
5.42-6.640.02435.179328340298.2
6.64-9.390.01846.17431267198
9.390.01353.954037148396.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.07 Å
Translation3 Å49.07 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z7e

1z7e


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.1933 / WRfactor Rwork: 0.1595 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8531 / SU B: 10.538 / SU ML: 0.125 / SU R Cruickshank DPI: 0.2031 / SU Rfree: 0.1734 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 6444 5 %RANDOM
Rwork0.177 ---
obs0.1793 128096 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.83 Å2 / Biso mean: 30.9176 Å2 / Biso min: 6.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.9 Å20 Å21.27 Å2
2---0.87 Å20 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15337 0 12 881 16230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215713
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.94621348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.68751961
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61124.132714
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.424152500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7781580
X-RAY DIFFRACTIONr_chiral_restr0.0910.22358
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112040
X-RAY DIFFRACTIONr_mcbond_it0.7031.59792
X-RAY DIFFRACTIONr_mcangle_it1.269215705
X-RAY DIFFRACTIONr_scbond_it2.13235921
X-RAY DIFFRACTIONr_scangle_it3.4134.55642
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 480 -
Rwork0.251 8951 -
all-9431 -
obs--99.32 %
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)
10.43090.095-0.05730.69680.18350.28980.0188-0.00810.02720.0938-0.0109-0.05880.00570.0159-0.00790.076-0.017-0.02080.03680.00420.0294-0.5495-7.0842-13.3773
20.43640.02150.12470.75390.17210.56330.0023-0.0137-0.02-0.0377-0.01070.14310.112-0.02060.00840.0811-0.04420.01960.0399-0.00240.0813-37.7247-51.1976-37.7147
30.34260.10620.24650.3979-0.17860.35370.03030.0375-0.047-0.0298-0.0238-0.07050.03630.0429-0.00650.04660.00940.04040.0558-0.0060.05881.2648-48.8982-37.3527
40.5316-0.1055-0.12950.3664-0.16190.9397-0.01820.06450.0187-0.0787-0.0415-0.0327-0.10770.12410.05970.1296-0.070.01140.07220.01850.0145-2.4771-7.6523-61.3343
50.6063-0.1818-0.12980.5845-0.10740.14640.00180.0508-0.0324-0.1053-0.01380.1013-0.0487-0.01080.01210.1142-0.0153-0.06230.03570.00090.0372-41.7034-8.597-59.0758
60.6153-0.01060.15750.23690.2210.78730.0221-0.036-0.01060.063-0.03860.0626-0.0082-0.11920.01650.06820.00680.04140.0454-0.01820.0458-39.5185-10.105-13.1271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 348
2X-RAY DIFFRACTION1A352 - 353
3X-RAY DIFFRACTION1A354 - 874
4X-RAY DIFFRACTION2B2 - 348
5X-RAY DIFFRACTION2B352 - 353
6X-RAY DIFFRACTION2B354 - 840
7X-RAY DIFFRACTION3C2 - 348
8X-RAY DIFFRACTION3C352 - 353
9X-RAY DIFFRACTION3C354 - 844
10X-RAY DIFFRACTION4D2 - 348
11X-RAY DIFFRACTION4D352 - 353
12X-RAY DIFFRACTION4D354 - 860
13X-RAY DIFFRACTION5E2 - 348
14X-RAY DIFFRACTION5E352 - 353
15X-RAY DIFFRACTION5E354 - 862
16X-RAY DIFFRACTION6F2 - 345
17X-RAY DIFFRACTION6F352 - 353
18X-RAY DIFFRACTION6F354 - 881

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