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- PDB-4mg4: Crystal structure of a putative phosphonomutase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 4mg4
TitleCrystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315
ComponentsPhosphonomutase
KeywordsUNKNOWN FUNCTION / SSGCID / NIAID / Structural Genomics / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative phosphonomutase from Burkholderia cenocepacia J2315
Authors: Lukacs, C.M. / Edwards, T.E. / Lorimer, D.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 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

Downloads & links

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Assembly

Deposited unit
A: Phosphonomutase
B: Phosphonomutase
C: Phosphonomutase
D: Phosphonomutase
E: Phosphonomutase
F: Phosphonomutase
G: Phosphonomutase
H: Phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,72937
Polymers221,5958
Non-polymers1,13529
Water32,3731797
1
A: Phosphonomutase
H: Phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6739
Polymers55,3992
Non-polymers2757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-93 kcal/mol
Surface area19180 Å2
MethodPISA
2
B: Phosphonomutase
F: Phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6739
Polymers55,3992
Non-polymers2757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-85 kcal/mol
Surface area19330 Å2
MethodPISA
3
C: Phosphonomutase
E: Phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70910
Polymers55,3992
Non-polymers3108
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-95 kcal/mol
Surface area19290 Å2
MethodPISA
4
D: Phosphonomutase
G: Phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6739
Polymers55,3992
Non-polymers2757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-94 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.600, 91.180, 110.010
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phosphonomutase


Mass: 27699.352 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: BceJ2315_40480, BCAM0587 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EL08
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 1797 / 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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: JCSG+c2: 20% PEG6000, 1M LiCl, 0.1M NaCit pH4.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9798 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 236885 / Num. obs: 236354 / % possible obs: 99.8 % / Redundancy: 3.76 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.15
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3.51 / Num. unique all: 17451 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZE3

2ze3


Resolution: 1.7→46.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.192 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18912 11843 5 %RANDOM
Rwork0.15752 ---
obs0.15911 224512 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.66 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14455 0 41 1797 16293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214144
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.96220327
X-RAY DIFFRACTIONr_angle_other_deg0.855332242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46652020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96422.864597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.925152119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.15915135
X-RAY DIFFRACTIONr_chiral_restr0.0960.22367
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02117485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023354
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3171.4388065
X-RAY DIFFRACTIONr_mcbond_other1.3171.4388064
X-RAY DIFFRACTIONr_mcangle_it2.0642.14810090
X-RAY DIFFRACTIONr_mcangle_other2.0642.14810091
X-RAY DIFFRACTIONr_scbond_it2.1151.6916828
X-RAY DIFFRACTIONr_scbond_other2.1141.6916828
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3192.44110238
X-RAY DIFFRACTIONr_long_range_B_refined6.04213.50518519
X-RAY DIFFRACTIONr_long_range_B_other6.04213.50518519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 864 -
Rwork0.201 16560 -
obs--99.91 %
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)
10.37830.08760.18960.18160.12730.40880.0294-0.0160.0156-0.0553-0.0530.0184-0.00110.03010.02360.04540.0309-0.00410.0412-0.01420.0223253.4072-11.5183143.5849
20.36440.0288-0.14560.2250.01280.28960.01650.0292-0.01550.0096-0.0074-0.0045-0.0158-0.0143-0.00910.02050.00050.00350.0536-0.04120.0343247.184611.4507180.3634
30.46890.0424-0.23810.2072-0.02750.19130.0164-0.017-0.0524-0.0191-0.03010.0388-0.05130.02190.01370.0325-0.00690.00620.0453-0.02860.0367246.2439-37.2711181.4298
40.33460.03240.25040.22020.21040.6477-0.01420.03210.00460.01160.00910.0642-0.00360.07120.00520.05340.0248-0.00330.049-0.01230.0295239.153922.5631218.2046
50.69020.1139-0.15740.4815-0.07690.12530.02680.02630.06220.07620.0293-0.00280.0143-0.0194-0.05610.024-0.0054-0.00410.0241-0.02410.0768211.4067-47.2264194.1968
60.75020.1689-0.12410.25690.01640.11720.0060.0301-0.03770.04040.05190.01070.00750.0158-0.0580.0187-0.0021-0.0150.0403-0.0020.0887212.7849-0.0204193.7313
70.4808-0.03480.13140.10740.0490.32670.0302-0.03560.0574-0.0444-0.05340.00790.02050.00110.02330.03630.01970.00340.0425-0.01820.0363251.644831.7042253.7621
80.25360.00060.23140.17080.361.4962-0.17370.02530.00330.03450.03620.08710.00240.14210.13760.13730.00160.00680.02590.01340.0496241.0057-23.8843108.3548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 253
2X-RAY DIFFRACTION2B1 - 253
3X-RAY DIFFRACTION3C1 - 253
4X-RAY DIFFRACTION4D4 - 251
5X-RAY DIFFRACTION5E1 - 253
6X-RAY DIFFRACTION6F3 - 252
7X-RAY DIFFRACTION7G2 - 253
8X-RAY DIFFRACTION8H5 - 252

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