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- PDB-4gib: 2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB)... -

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Basic information

Entry
Database: PDB / ID: 4gib
Title2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / Rossmann fold / HAD-like / beta-Phosphoglucomutase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / hydrolase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / 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 ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / 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
GLYCINE / PHOSPHATE ION / Beta-phosphoglucomutase (Beta-D-Glucose 1,6-phosphomutase)
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,17212
Polymers56,5302
Non-polymers64210
Water3,063170
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6717
Polymers28,2651
Non-polymers4066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5015
Polymers28,2651
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.807, 51.364, 79.442
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-phosphoglucomutase / / Beta-D-Glucose 1 / 6-phosphomutase


Mass: 28264.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_21890, pgmB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q185X7, beta-phosphoglucomutase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein: 7.6mg/mL, 0.25M Sodium cloride, 0.01M Tris-HCl, pH 8.3. Screen: PACT (A3), 0.1M SPG buffer, pH 6.0, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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: Mar 16, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.27→30 Å / Num. all: 21526 / Num. obs: 21526 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.7
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1055 / % possible all: 97.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z4N

1z4n


Resolution: 2.27→29.92 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.788 / SU ML: 0.114
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25911 1099 5.1 %RANDOM
Rwork0.1928 ---
all0.1962 20343 --
obs0.1962 20343 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å22.12 Å2
2---1.64 Å2-0 Å2
3---2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.27→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 34 170 3750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223709
X-RAY DIFFRACTIONr_bond_other_d0.0010.022493
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9635004
X-RAY DIFFRACTIONr_angle_other_deg0.79736127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3815461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72425.801181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31315691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1861513
X-RAY DIFFRACTIONr_chiral_restr0.080.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024144
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02711
X-RAY DIFFRACTIONr_mcbond_it0.9981.52271
X-RAY DIFFRACTIONr_mcbond_other0.2861.5930
X-RAY DIFFRACTIONr_mcangle_it1.72323664
X-RAY DIFFRACTIONr_scbond_it3.11431438
X-RAY DIFFRACTIONr_scangle_it4.554.51340
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 67 -
Rwork0.227 1442 -
obs-1442 95.99 %
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)
11.5972-1.0876-0.64913.74050.98992.1697-0.06280.0795-0.065-0.09880.0330.23670.05670.1210.02990.0132-0.0142-0.00590.0756-0.01740.04740.96180.78523.1136
23.53980.36380.68675.09562.35322.6951-0.01510.29590.1136-0.5872-0.0620.0116-0.251-0.1110.07710.07680.02210.01350.05950.02570.02844.734417.052332.0551
310.0544.80366.56362.30173.17256.3790.0687-0.49130.06290.029-0.22540.013-0.1786-0.37240.15660.05470.0016-0.00820.10170.00440.0904-1.276510.856640.1627
41.09090.10830.26410.53660.6781.46720.0146-0.0345-0.108-0.007-0.01330.07160.1388-0.0711-0.00120.0519-0.00340.0020.01650.01540.07693.2057-6.982125.7749
52.4926-0.2549-0.11812.45390.09653.49630.10640.37140.1004-0.3038-0.1385-0.12820.07060.03940.03210.0480.01230.01930.11030.02120.010310.3602-3.534311.6162
61.11120.32840.40724.1432-2.41211.7850.08260.0498-0.16610.1547-0.1616-0.2688-0.12270.08790.07910.13530.02950.02480.101-0.02260.1104-19.985214.778721.0806
72.90590.8041-0.6035.8272-2.14185.81130.22480.2157-0.02050.20740.07650.2616-0.3632-0.2671-0.30130.03620.02440.02320.0491-0.00210.1447-30.72738.252426.5122
81.5860.08260.16531.9828-0.35291.8457-0.0237-0.02160.04910.2419-0.02370.0619-0.1607-0.08730.04740.04810.00680.01150.0159-0.00760.0157-21.899328.56520.8167
95.80740.6983-2.03054.19310.87073.6677-0.13830.1996-0.3257-0.4946-0.16710.1160.217-0.29910.30530.1465-0.0044-0.0050.1376-0.02220.0352-24.790123.62515.4432
108.9817-4.27632.78566.6113-1.63715.36020.18960.80640.4034-0.8031-0.2292-0.25060.02720.12060.03960.2378-0.00450.07180.20390.01410.0477-17.046931.26270.8646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 24
2X-RAY DIFFRACTION2A25 - 64
3X-RAY DIFFRACTION3A65 - 87
4X-RAY DIFFRACTION4A88 - 161
5X-RAY DIFFRACTION5A162 - 224
6X-RAY DIFFRACTION6B1 - 39
7X-RAY DIFFRACTION7B40 - 76
8X-RAY DIFFRACTION8B77 - 161
9X-RAY DIFFRACTION9B162 - 199
10X-RAY DIFFRACTION10B200 - 223

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