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- PDB-4eo9: Crystal structure of a phosphoglycerate mutase gpm1 from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 4eo9
TitleCrystal structure of a phosphoglycerate mutase gpm1 from Mycobacterium leprae
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / glycolysis / pathogenic bacterium
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / glycolytic process / gluconeogenesis
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionApr 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8392
Polymers29,8041
Non-polymers351
Water1,47782
1
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules

A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6784
Polymers59,6072
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z1
Buried area2120 Å2
ΔGint-25 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.310, 80.310, 119.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase / BPG-dependent PGAM / PGAM / Phosphoglyceromutase / dPGM


Mass: 29803.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: BR4923 / Gene: gpmA, MLBr02441 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZT86, EC: 5.4.2.1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyleA.00184.a.A1 PS01437 at 18.1 mg/mL against JCSG+ A8 0.2 M ammonium formate, 20% PEG 3350 supplemented with 15% PEG 400 as cryo-protectant, crystal tracking ID 233299a8, pH 7.5, VAPOR ...Details: MyleA.00184.a.A1 PS01437 at 18.1 mg/mL against JCSG+ A8 0.2 M ammonium formate, 20% PEG 3350 supplemented with 15% PEG 400 as cryo-protectant, crystal tracking ID 233299a8, pH 7.5, 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: Apr 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 15013 / Num. obs: 14961 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 45.491 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.45-2.510.52947634108399.7
2.51-2.580.4524.597364103699.8
2.58-2.660.3675.6472691028100
2.66-2.740.3046.637066100199.9
2.74-2.830.2547.46682796499.8
2.83-2.930.2288.356695941100
2.93-3.040.16710.8642990499.9
3.04-3.160.11914.69624488399.9
3.16-3.30.10216.635946837100
3.3-3.460.08520.625701810100
3.46-3.650.06328.815514784100
3.65-3.870.05434.58500472399.9
3.87-4.140.04437.89480969399.7
4.14-4.470.03645.31432964999.7
4.47-4.90.03646.68411259899.3
4.9-5.480.03740.333774551100
5.48-6.330.03838.743350498100
6.33-7.750.03442.742790420100
7.75-10.960.02157.492195348100
10.960.01764.7111021095.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å38.06 Å
Translation3 Å38.06 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.1982 / WRfactor Rwork: 0.1632 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8647 / SU B: 11.464 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2705 / SU Rfree: 0.2174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 755 5 %RANDOM
Rwork0.1958 ---
obs0.1976 14960 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.21 Å2 / Biso mean: 39.0887 Å2 / Biso min: 18.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1861 0 1 82 1944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191921
X-RAY DIFFRACTIONr_bond_other_d0.0010.021288
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9682630
X-RAY DIFFRACTIONr_angle_other_deg1.01933117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1595243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10822.52987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58215294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.781520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212165
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02411
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 48 -
Rwork0.291 903 -
all-951 -
obs--99.69 %
Refinement TLS params.Method: refined / Origin x: -23.6009 Å / Origin y: 4.6014 Å / Origin z: -16.5861 Å
111213212223313233
T0.1846 Å20.0521 Å20.0778 Å2-0.1175 Å2-0.0509 Å2--0.113 Å2
L0.2314 °2-0.3763 °2-0.172 °2-0.905 °20.3198 °2--1.5644 °2
S0.1785 Å °0.0464 Å °0.0786 Å °-0.1541 Å °-0.0457 Å °-0.0666 Å °-0.1092 Å °0.1425 Å °-0.1327 Å °

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