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- PDB-4oo0: Crystal Structure of Maf-like protein BceJ2315_23540 from Burkhol... -

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Basic information

Entry
Database: PDB / ID: 4oo0
TitleCrystal Structure of Maf-like protein BceJ2315_23540 from Burkholderia cenocepacia
ComponentsMaf-like protein BCAL2394
KeywordsHYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Maf-like protein
Function / homology
Function and homology information


dTTP diphosphatase activity / NADH pyrophosphatase activity / nucleotide diphosphatase / nucleotide metabolic process / cytoplasm
Similarity search - Function
Nucleoside triphosphate pyrophosphatase Maf-like protein / Maf-like protein / Maf protein - #10 / Inosine triphosphate pyrophosphatase-like / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / dTTP/UTP pyrophosphatase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Maf-like protein BceJ2315_23540 from Burkholderia cenocepacia
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Maf-like protein BCAL2394
B: Maf-like protein BCAL2394
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,05513
Polymers50,1092
Non-polymers94611
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-44 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.200, 84.200, 260.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-431-

HOH

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Components

#1: Protein Maf-like protein BCAL2394


Mass: 25054.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL2394 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E5S2
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+(a6): 20% PEG-1000, 100mM Sodium phosphate dibasic/ citric acid, pH=4.2, 200mM Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 30813 / Num. obs: 30677 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 40.829 Å2 / Rmerge(I) obs: 0.06 / Χ2: 0.959 / Net I/σ(I): 25.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.5454.220722220799.6
2.21-2.270.4385.2220121214099.8
2.27-2.330.3696.2419730210899.8
2.33-2.40.2837.8819072204699.8
2.4-2.480.2259.9218596199299.8
2.48-2.570.18911.617777191099.8
2.57-2.670.16213.4117155185599.8
2.67-2.780.13716.116506179599.9
2.78-2.90.121.0815873174799.5
2.9-3.040.07626.5114984165899.8
3.04-3.210.06131.8214069156599.6
3.21-3.40.04938.513281151099.7
3.4-3.630.0446.0212317142399.6
3.63-3.930.03551.2911423132699.8
3.93-4.30.03156.310495124199.4
4.3-4.810.02861.399590112899.6
4.81-5.550.02957.778449101599.5
5.55-6.80.0356.47714287699.4
6.8-9.620.02664.96549170798.7
9.620.02558.03271242891.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EX2

1ex2


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2106 / WRfactor Rwork: 0.1675 / FOM work R set: 0.8527 / SU B: 8.116 / SU ML: 0.112 / SU R Cruickshank DPI: 0.1789 / SU Rfree: 0.1644 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 1534 5 %RANDOM
Rwork0.1769 ---
all0.1791 32122 --
obs0.1791 30588 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 41.105 Å2 / Biso min: 11.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å2-0 Å2
2--0.22 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3040 0 52 223 3315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193164
X-RAY DIFFRACTIONr_bond_other_d0.0010.023077
X-RAY DIFFRACTIONr_angle_refined_deg1.7392.0034313
X-RAY DIFFRACTIONr_angle_other_deg0.7837034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2625416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77122.097124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43715479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1191535
X-RAY DIFFRACTIONr_chiral_restr0.0730.2505
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213590
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02681
X-RAY DIFFRACTIONr_mcbond_it1.212.3361661
X-RAY DIFFRACTIONr_mcbond_other1.2072.3351660
X-RAY DIFFRACTIONr_mcangle_it1.9893.4932078
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 111 -
Rwork0.223 2094 -
all-2205 -
obs--99.59 %
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)
12.7274-0.6491-0.37432.5741-0.54542.9790.1915-0.2199-0.3946-0.08390.17540.29710.0974-0.4233-0.36690.1056-0.0836-0.15110.28210.09410.27417.127327.16663.8071
21.8471-1.10840.84321.6222-0.5291.05690.026-0.4214-0.18660.20190.0620.1121-0.1253-0.1829-0.0880.0922-0.0299-0.02860.26340.05120.078216.218842.7778.5049
34.05430.76510.07941.5416-0.632.8670.07960.250.0376-0.1424-0.0402-0.1003-0.12740.0608-0.03940.12540.0510.03960.11040.02830.075510.990651.0558-21.9929
41.3113-0.40110.55960.8377-0.41271.19950.03990.11540.08640.0242-0.0485-0.211-0.18650.26390.00860.0651-0.00590.0130.1860.02930.089823.273350.2757-15.7981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 52
2X-RAY DIFFRACTION2A53 - 215
3X-RAY DIFFRACTION3B12 - 57
4X-RAY DIFFRACTION4B58 - 215

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