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- PDB-3lnt: Crystal structure of phosphoglyceromutase from Burkholderia Pseud... -

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Basic information

Entry
Database: PDB / ID: 3lnt
TitleCrystal structure of phosphoglyceromutase from Burkholderia Pseudomallei 1710B with bound malonic acid
Components2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
KeywordsISOMERASE / mutase / phosphoglycerylmutase / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Glycolysis
Function / homology
Function and homology information


2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / gluconeogenesis / glycolytic process
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
MALONATE ION / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase.
Authors: Davies, D.R. / Staker, B.L. / Abendroth, J.A. / Edwards, T.E. / Hartley, R. / Leonard, J. / Kim, H. / Rychel, A.L. / Hewitt, S.N. / Myler, P.J. / Stewart, L.J.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4438
Polymers56,0302
Non-polymers4136
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2024
Polymers28,0151
Non-polymers1873
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2414
Polymers28,0151
Non-polymers2263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.620, 119.620, 103.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 28014.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: gpmA, BURPS1710b_0662 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JWH7, EC: 5.4.2.1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M SODIUM MALONATE, PH 7.0. Crystal transferred to 2.4 M Malonate, pH 7.0 plus 25% (v/v) Ethylene Glycol for Cryoprotection, 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: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→46.34 Å / Num. obs: 49080 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.37 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.88
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.918 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2481 5.1 %RANDOM
Rwork0.17 ---
obs0.172 49078 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 27 256 4048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223928
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9635355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1795486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93623.476187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21715644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0391534
X-RAY DIFFRACTIONr_chiral_restr0.0920.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213038
X-RAY DIFFRACTIONr_mcbond_it0.7381.52387
X-RAY DIFFRACTIONr_mcangle_it1.32423850
X-RAY DIFFRACTIONr_scbond_it2.17931541
X-RAY DIFFRACTIONr_scangle_it3.4834.51498
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 189 -
Rwork0.222 3405 -
obs--99.89 %
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)
10.65470.04870.09580.45510.27450.64990.01210.0967-0.0241-0.00940.0049-0.0242-0.03220.044-0.0170.0587-0.00030.01080.0786-0.01390.0773-28.2611-23.4626-7.5301
23.84152.2986-0.93864.4591-1.81271.3977-0.0370.0032-0.18790.37190.0137-0.3278-0.20790.2260.02340.077-0.038-0.03990.1354-0.04610.0906-14.9641-11.71819.43
30.76350.13340.07831.24550.80711.12730.0038-0.0577-0.06230.09370.0245-0.09750.07260.0459-0.02830.05970.00810.00190.04820.00640.0746-27.0607-24.83468.7168
41.0219-0.0146-0.11170.63060.03350.7047-0.0117-0.0428-0.1914-0.00730.0577-0.0144-0.0130.1103-0.0460.03090.02710.020.05930.00310.1296-17.2783-36.1021-1.9443
55.090.67-0.06672.19070.92130.41230.00210.082-0.00770.1420.0275-0.05910.06350.0096-0.02960.04910.02610.02870.0834-0.00040.0961-10.4439-24.7451-10.9749
60.7513-0.16670.53980.44690.23091.0518-0.06820.01810.0529-0.05690.0761-0.0079-0.0871-0.0088-0.00780.0846-0.005-0.01260.06810.01810.0507-47.2729-17.9332-14.428
71.5750.6912-0.23180.32060.08062.0071-0.06120.11240.0661-0.0430.050.0338-0.28090.22790.01120.1598-0.0117-0.05530.07440.0010.0384-60.0363-24.264-36.2654
82.34030.18210.94010.90241.20071.84810.29010.0473-0.33210.0099-0.0734-0.08910.1165-0.1483-0.21680.0712-0.0167-0.06430.10140.01250.0688-56.1488-34.3249-23.2371
90.06910.2667-0.2621.65250.05773.18360.0091-0.00430.03030.00770.03230.2171-0.0951-0.1047-0.04130.02750.0255-0.01520.13220.0450.0789-56.0395-24.1784-5.1987
104.66270.99251.68340.43070.75161.5026-0.20260.00040.2547-0.09970.00360.159-0.2103-0.23230.1990.03680.0468-0.02570.21960.09470.1265-63.4265-15.8646-10.7778
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION2A88 - 108
3X-RAY DIFFRACTION3A109 - 187
4X-RAY DIFFRACTION4A188 - 227
5X-RAY DIFFRACTION5A228 - 244
6X-RAY DIFFRACTION6B1 - 88
7X-RAY DIFFRACTION7B89 - 114
8X-RAY DIFFRACTION8B115 - 161
9X-RAY DIFFRACTION9B162 - 186
10X-RAY DIFFRACTION10B187 - 229

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