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- PDB-3uw2: X-ray Crystal Structure of Phosphoglucomutase/phosphomannomutase ... -

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Basic information

Entry
Database: PDB / ID: 3uw2
TitleX-ray Crystal Structure of Phosphoglucomutase/phosphomannomutase family protein (BTH_I1489)from Burkholderia thailandensis
ComponentsPhosphoglucomutase/phosphomannomutase family protein
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Phosphoglucomutase / Phosphorylation / S109
Function / homology
Function and homology information


intramolecular phosphotransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III ...Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphoglucomutase/phosphomannomutase family protein
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.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

Downloads & links

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Assembly

Deposited unit
A: Phosphoglucomutase/phosphomannomutase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,09311
Polymers52,3761
Non-polymers71710
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.376, 75.233, 104.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoglucomutase/phosphomannomutase family protein


Mass: 52376.254 Da / Num. of mol.: 1 / Fragment: Phosphoglucomutase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I1489 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SYG4

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Non-polymers , 5 types, 341 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: JCSG+ Well B9: 0.1 M Citric Acid pH 4.0, 20% PEG 6000. ButhA.01370.a.A1 PS01178 CR_24 Peak2, 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: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.95→61.04 Å / Num. obs: 39125 / % possible obs: 99.2 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.063 / Χ2: 1.036 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.025.40.48137120.819195.8
2.02-2.15.40.38838480.861198.9
2.1-2.25.40.29839001.0041100
2.2-2.315.40.23538721.1081100
2.31-2.465.40.17638911.061100
2.46-2.655.40.1239280.9731100
2.65-2.915.40.09439461.1631100
2.91-3.335.40.07339221.589199.9
3.33-4.25.30.03939961.062199.6
4.2-505.10.02741100.708198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→61.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Occupancy max: 1 / Occupancy min: 0.39 / SU B: 7.613 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1967 5 %RANDOM
Rwork0.1769 ---
obs0.1791 39077 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.51 Å2 / Biso mean: 41.737 Å2 / Biso min: 13.68 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å20 Å2
2---2.86 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.95→61.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 41 331 3806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193569
X-RAY DIFFRACTIONr_angle_refined_deg1.8571.9764843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2125468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90923.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07715548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0491531
X-RAY DIFFRACTIONr_chiral_restr0.1250.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212756
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 138 -
Rwork0.239 2388 -
all-2526 -
obs--94.29 %
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)
14.65170.21430.14029.1289-1.28333.33790.1721-0.05540.02910.1753-0.1057-0.80550.27940.3081-0.06630.06860.0251-0.04120.0442-0.01490.08829.803-13.4292-7.3138
20.73070.15790.00361.2155-0.0131.72990.0109-0.01450.07310.0991-0.00530.0001-0.1155-0.1282-0.00570.06370.02070.02170.0642-0.00910.0882-2.769-9.6081-12.9434
30.3272-0.379-0.26532.8950.01561.4168-0.0299-0.0365-0.0548-0.32770.0498-0.12110.1075-0.0292-0.01990.1154-0.03050.06480.0303-0.01560.06244.1738-20.6914-35.6233
40.68950.2012-0.54061.5264-0.10091.0849-0.0877-0.0462-0.0595-0.1872-0.0036-0.13120.08740.05560.09130.10360.02920.04760.04140.02050.052710.0866-3.0367-37.5674
539.1312-4.7094-8.875814.1963-8.2948.4756-1.7861-4.76971.77521.1311.1378-1.674-0.10811.02410.64830.57190.8075-0.47742.4843-0.84070.475631.93086.349-19.4974
63.9758-1.781-3.29545.50774.0688.8866-0.5313-1.09460.22060.37050.6368-0.22281.18251.4418-0.10550.18270.23110.03580.5840.01010.19431.4730.6402-30.0111
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 26
2X-RAY DIFFRACTION2A27 - 158
3X-RAY DIFFRACTION3A159 - 248
4X-RAY DIFFRACTION4A249 - 378
5X-RAY DIFFRACTION5A385 - 396
6X-RAY DIFFRACTION6A397 - 464

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