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- PDB-4pza: The complex structure of mycobacterial glucosyl-3-phosphoglycerat... -

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Basic information

Entry
Database: PDB / ID: 4pza
TitleThe complex structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c with inorganic phosphate
ComponentsGlucosyl-3-phosphoglycerate phosphatase
KeywordsHYDROLASE / alpha/beta/alpha sandwich / glycolysis
Function / homology
Function and homology information


glucosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase / mannosyl-3-phosphoglycerate phosphatase activity / cytoplasm
Similarity search - Function
: / 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
PHOSPHATE ION / Glucosyl-3-phosphoglycerate phosphatase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.776 Å
AuthorsZhou, W.H. / Zheng, Q.Q. / Jiang, D.Q. / Zhang, W. / Zhang, Q.Q. / Jin, J. / Li, X. / Yang, H.T. / Shaw, N. / Rao, Z.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanism of dephosphorylation of glucosyl-3-phosphoglycerate by a histidine phosphatase
Authors: Zheng, Q. / Jiang, D. / Zhang, W. / Zhang, Q. / Zhao, Q. / Jin, J. / Li, X. / Yang, H. / Bartlam, M. / Shaw, N. / Zhou, W. / Rao, Z.
History
DepositionMar 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glucosyl-3-phosphoglycerate phosphatase
B: Glucosyl-3-phosphoglycerate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5984
Polymers48,4092
Non-polymers1902
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-19 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.358, 76.893, 105.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucosyl-3-phosphoglycerate phosphatase / GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP / Glucosyl-3-phosphoglycerate phosphatase / ...GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP / Glucosyl-3-phosphoglycerate phosphatase / GpgP / Mannosyl-3-phosphoglycerate phosphatase / MpgP


Mass: 24204.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: gpgP, MT2492, Rv2419c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WIC6, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, mannosyl-3-phosphoglycerate phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, pH 7.5, 10% 2-propanol, 20% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 44618 / Num. obs: 44306 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 21.25 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.063 / Net I/σ(I): 29.5
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.58 / Num. unique all: 2187 / Rsym value: 0.303 / % possible all: 89.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2E

1h2e


Resolution: 1.776→36.142 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 20.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2187 1999 4.52 %
Rwork0.1824 --
obs0.1841 44235 99.55 %
all-44434 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.776→36.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 10 386 3646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073326
X-RAY DIFFRACTIONf_angle_d1.1724529
X-RAY DIFFRACTIONf_dihedral_angle_d14.5781193
X-RAY DIFFRACTIONf_chiral_restr0.084501
X-RAY DIFFRACTIONf_plane_restr0.005591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7756-1.820.29231360.2233285496
1.82-1.86920.2381410.20292998100
1.8692-1.92420.23261420.19752989100
1.9242-1.98630.25691400.18932979100
1.9863-2.05730.22591430.18122994100
2.0573-2.13960.24821420.17892995100
2.1396-2.2370.21161410.18432986100
2.237-2.35490.24261430.18373022100
2.3549-2.50240.23251430.18643013100
2.5024-2.69560.2121420.19463022100
2.6956-2.96670.2261450.19533050100
2.9667-3.39570.21891440.18123056100
3.3957-4.27720.19641480.16173097100
4.2772-36.14980.19731490.1784318198
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)
11.0371-0.0062-0.09872.2686-0.15211.05710.0127-0.11680.18420.39240.0770.1539-0.163-0.0953-0.07990.19360.01540.04390.1785-0.01380.2114-2.337418.459933.7431
21.086-0.5808-0.25371.9385-0.38242.261-0.05040.0566-0.00590.1205-0.02880.1242-0.08350.00170.04010.1364-0.03040.00810.1542-0.00760.158-1.11126.315326.5065
31.7692-0.2258-0.10971.5383-0.75471.37160.02250.0360.0261-0.04170.01050.0022-0.0017-0.0013-0.02460.11230.00430.00160.12290.00410.12476.081311.433723.5805
41.2709-0.18890.42911.9684-0.15483.1005-0.02450.15240.1006-0.2239-0.0258-0.0896-0.13290.34730.05920.1577-0.01920.01350.1761-0.01180.169225.433819.819418.4098
50.68850.168-0.12371.9196-0.02410.8759-0.04160.04110.0305-0.20090.0563-0.1064-0.03820.1377-0.01720.155-0.01950.02840.1972-0.00860.155828.88916.078416.5279
61.51880.04860.15381.50170.06880.83-0.0142-0.12550.02350.22060.0373-0.0553-0.03660.0969-0.02180.14630.0039-0.00210.1611-0.01080.124523.957812.386531.1078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:108)
2X-RAY DIFFRACTION2(chain A and resid 109:150)
3X-RAY DIFFRACTION3(chain A and resid 151:219)
4X-RAY DIFFRACTION4(chain B and resid 2:22)
5X-RAY DIFFRACTION5(chain B and resid 23:132)
6X-RAY DIFFRACTION6(chain B and resid 133:218)

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