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- PDB-3dv9: Putative beta-phosphoglucomutase from Bacteroides vulgatus. -

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Basic information

Entry
Database: PDB / ID: 3dv9
TitlePutative beta-phosphoglucomutase from Bacteroides vulgatus.
Componentsbeta-phosphoglucomutase
KeywordsISOMERASE / structural genomics / APC60149 / beta-phosphoglucomutase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative beta-phosphoglucomutase
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsOsipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative beta-phosphoglucomutase from Bacteroides vulgatus.
Authors: Osipiuk, J. / Tesar, C. / Clancy, S. / Joachimiak, A.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 2024Group: 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_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_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_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: beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0804
Polymers27,8981
Non-polymers1813
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.247, 100.161, 38.991
Angle α, β, γ (deg.)90.000, 97.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-333-

HOH

31A-400-

HOH

41A-479-

HOH

Detailsputative biological unit is the same as asym.

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Components

#1: Protein beta-phosphoglucomutase


Mass: 27898.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_4110 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6L7P8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M magnesium formate, 15% PEG-3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 12, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.72→26.9 Å / Num. all: 25739 / Num. obs: 25739 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 28.9
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1296 / % possible all: 94.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→26.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 4.348 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1312 5.1 %RANDOM
Rwork0.169 ---
all0.171 25732 --
obs0.171 25732 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.15 Å2 / Biso mean: 24.153 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20.25 Å2
2---0.43 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.72→26.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1896 0 10 239 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222082
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9632832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5925276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2425.05199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30515375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.018159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021596
X-RAY DIFFRACTIONr_nbd_refined0.2060.21021
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21391
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.224
X-RAY DIFFRACTIONr_mcbond_it0.8081.51319
X-RAY DIFFRACTIONr_mcangle_it1.28422064
X-RAY DIFFRACTIONr_scbond_it2.0423854
X-RAY DIFFRACTIONr_scangle_it3.1684.5753
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 93 -
Rwork0.239 1702 -
all-1795 -
obs-1795 94.23 %
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)
15.63198.251.226713.7509-1.512615.3778-0.3464-0.0452-0.56320.1896-0.0735-1.47021.23241.1970.41990.116-0.02560.0409-0.00760.00440.13819.271868.50210.9226
22.6909-2.03911.42051.7943-1.3151.99380.079-0.0283-0.02750.17160.00280.14290.2929-0.1245-0.0818-0.008-0.08260.0211-0.07790.0021-0.04878.240870.67429.684
31.91291.38640.9911.51581.14171.06820.00760.05350.1435-0.017-0.04170.1598-0.0711-0.10290.0341-0.0692-0.0063-0.0052-0.02180.0036-0.077415.376884.45935.4676
41.5879-1.2605-0.98296.08870.84940.60940.01080.2645-0.10720.1436-0.11790.2065-0.113-0.12870.10710.05920.0422-0.0256-0.0565-0.0037-0.044817.26104.94925.0693
56.10120.869-1.40193.12960.87950.7096-0.1846-0.1156-0.1120.20920.08770.46540.18730.19920.0969-0.01470.023-0.021-0.0544-0.0478-0.04889.66199.57321.1627
61.27611.4576-2.48343.5388-2.13035.0992-0.1998-0.1823-0.05610.1970.08360.76480.3202-0.43190.11610.27920.03230.08970.0552-0.03730.3351.8535107.891426.2483
77.9824-0.1962-1.53526.4298-0.12881.9953-0.13960.38160.1485-0.5151-0.07450.5694-0.3593-0.13080.21410.12130.0531-0.0681-0.1592-0.0055-0.05487.6398113.779518.6326
826.9345-11.283-10.45437.68355.9897.59710.52930.92320.356-0.663-0.3852-0.7286-0.4397-0.0362-0.14410.14240.03080.0634-0.19320.0176-0.062121.6236109.18915.4887
94.34973.71613.65684.95953.69273.25550.0079-0.1716-0.06490.145-0.0304-0.08040.0534-0.14730.0225-0.05940.0183-0.0048-0.04770.0004-0.076429.35889.67617.093
102.37962.53742.03012.70562.16471.7319-0.110.1650.03510.07570.2093-0.0560.0527-0.2058-0.0993-0.06680.009-0.0002-0.03290.0001-0.093324.041582.1095-3.1324
118.715-2.0365-3.54143.86317.340114.13010.0436-0.2581.0552-0.5464-0.07790.4052-1.13080.01060.03430.0384-0.004-0.0151-0.00020.00720.062416.492394.90074.1441
1234.169214.7222-30.733143.87727.869242.58491.42460.84592.64370.7384-0.39972.7046-3.1333-0.3665-1.02490.14150.02850.05780.04590.08290.183724.9645100.53891.2253
136.46934.6508-4.060411.2859-0.10963.5423-0.14230.49370.3205-0.18490.10550.5904-0.2863-0.19350.0367-0.0462-0.00690.0054-0.01620.0345-0.07325.059395.0514-0.8235
1423.4955-5.6826-18.456311.506123.389979.0771.01831.41042.1127-0.63150.0973-1.3198-2.0323-0.0705-1.11560.16860.0783-0.01080.08860.12460.249313.198596.81510.3851
1510.26591.77031.21578.0249-8.322118.36980.07130.63490.9784-0.92750.35330.1082-1.9115-0.8107-0.42460.4690.0858-0.02020.14860.02130.29145.729999.21187.4099
161.5336-1.0684-0.87084.13263.42536.54090.02570.19080.3586-0.1763-0.08190.1967-0.2181-0.33970.0562-0.1182-0.0084-0.04320.00710.0203-0.0346.484989.28412.7324
170.56370.1075-0.19190.2023-0.3030.4556-0.0073-0.0146-0.00960.02860.00850.05830.0213-0.0355-0.0012-0.0655-0.0078-0.0048-0.0461-0.0095-0.059513.474184.757913.2297
183.7923-0.286-0.44990.02190.01860.9046-0.035-0.06660.03670.02090.0474-0.03010.09860.0064-0.0125-0.0447-0.0125-0.0051-0.04780.0002-0.073617.317381.004918.3338
190.1659-0.6199-0.86432.31653.234.50380.0121-0.2541-0.28690.04390.0287-0.13250.10170.0733-0.0408-0.04350.01-0.0091-0.06580.0194-0.041225.596777.24157.749
2037.3544-1.83482.54231.7653-3.62197.69630.03831.7802-1.3269-1.22350.360.03570.5122-0.0464-0.39830.1686-0.03180.00340.0896-0.0750.087617.942671.16330.6808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 31 - 6
2X-RAY DIFFRACTION2AA4 - 127 - 15
3X-RAY DIFFRACTION3AA13 - 3416 - 37
4X-RAY DIFFRACTION4AA35 - 5738 - 60
5X-RAY DIFFRACTION5AA58 - 7361 - 76
6X-RAY DIFFRACTION6AA74 - 8477 - 87
7X-RAY DIFFRACTION7AA85 - 9088 - 93
8X-RAY DIFFRACTION8AA91 - 10394 - 106
9X-RAY DIFFRACTION9AA104 - 115107 - 118
10X-RAY DIFFRACTION10AA116 - 122119 - 125
11X-RAY DIFFRACTION11AA123 - 135126 - 138
12X-RAY DIFFRACTION12AA136 - 140139 - 143
13X-RAY DIFFRACTION13AA141 - 149144 - 152
14X-RAY DIFFRACTION14AA150 - 155153 - 158
15X-RAY DIFFRACTION15AA156 - 162159 - 165
16X-RAY DIFFRACTION16AA163 - 179166 - 182
17X-RAY DIFFRACTION17AA180 - 211183 - 214
18X-RAY DIFFRACTION18AA212 - 228215 - 231
19X-RAY DIFFRACTION19AA229 - 237232 - 240
20X-RAY DIFFRACTION20AA238 - 243241 - 246

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