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- PDB-4g9b: Crystal structure of beta-phosphoglucomutase homolog from escheri... -

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Basic information

Entry
Database: PDB / ID: 4g9b
TitleCrystal structure of beta-phosphoglucomutase homolog from escherichia coli, target efi-501172, with bound mg, open lid
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / HAD / putative phosphoglucomutase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


DNA-mediated transformation / beta-phosphoglucomutase / beta-phosphoglucomutase activity / hydrolase activity / carbohydrate metabolic process / response to antibiotic / DNA damage response / magnesium ion binding / cytoplasm
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 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD 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 / haloacid dehalogenase-like hydrolase / 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
Unknown ligand / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of beta-phosphoglucomutase homolog from escherichia coli, target efi-501172, with bound mg, open lid
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Dunaway-Mariano, D. / Allen, K.N. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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)27,16411
Polymers26,6401
Non-polymers52410
Water3,243180
1
A: Beta-phosphoglucomutase
hetero molecules

A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,32922
Polymers53,2802
Non-polymers1,04820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area4810 Å2
ΔGint-160 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.168, 129.168, 85.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-407-

HOH

31A-410-

HOH

41A-431-

HOH

51A-437-

HOH

61A-448-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-phosphoglucomutase / / Beta-PGM


Mass: 26640.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: str. K-12 substr. MG1655 / Gene: ycjU, b1317, JW1310 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77366, beta-phosphoglucomutase

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Non-polymers , 6 types, 190 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffuction / pH: 7
Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.1 M Bis-Tris Propane:HCl, 1.8 M Magnesium Sulfate); Cryoprotection (Reservoir, + 20% glycerol), ...Details: Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl); Reservoir (0.1 M Bis-Tris Propane:HCl, 1.8 M Magnesium Sulfate); Cryoprotection (Reservoir, + 20% glycerol), sitting drop vapor diffuction, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX 225 HE / Detector: CCD / Date: Feb 3, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→68.063 Å / Num. all: 30181 / Num. obs: 30181 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.79110.8750.94809843680.875100
1.79-1.911.10.5561.44611741640.556100
1.9-2.0311.10.3252.44330038850.325100
2.03-2.1911.20.2023.74060436370.202100
2.19-2.411.20.1435.13742033460.143100
2.4-2.6911.20.1295.13414330490.129100
2.69-3.111.20.1234.93011226910.123100
3.1-3.811.20.08972556022910.089100
3.8-5.3810.90.05411.41947117810.05499.9
5.38-26.588100.04116.597159690.04196

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NAS

3nas


Resolution: 1.7→26.588 Å / Occupancy max: 1 / Occupancy min: 0.06 / FOM work R set: 0.8836 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 18.81 / Stereochemistry target values: ML
Details: THE STRUCTURE WAS REFINED UTILIZING THE STRUCTURE AND GEOMETRIC RESTRAINTS OF BENOZIC ACID, HOWEVER THE EXPERIMENTERS CAN NOT BE CERTAIN OF THE LIGANDS IDENTITY AS BENZOIC ACID WAS NOT A ...Details: THE STRUCTURE WAS REFINED UTILIZING THE STRUCTURE AND GEOMETRIC RESTRAINTS OF BENOZIC ACID, HOWEVER THE EXPERIMENTERS CAN NOT BE CERTAIN OF THE LIGANDS IDENTITY AS BENZOIC ACID WAS NOT A COMPONENT OF THE CRYSTALLIZATION OR PURIFICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 1527 5.06 %RANDOM
Rwork0.1655 ---
all0.1673 30180 --
obs0.1673 30180 99.85 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.53 Å2 / Biso mean: 27.8025 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 35 180 1943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071845
X-RAY DIFFRACTIONf_angle_d1.0192521
X-RAY DIFFRACTIONf_chiral_restr0.069283
X-RAY DIFFRACTIONf_plane_restr0.004326
X-RAY DIFFRACTIONf_dihedral_angle_d17.23661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.75490.27291460.253925642710100
1.7549-1.81760.27631280.220726022730100
1.8176-1.89040.24531460.195225702716100
1.8904-1.97640.20851530.180125712724100
1.9764-2.08050.19671350.166726072742100
2.0805-2.21080.19391220.165526092731100
2.2108-2.38140.17081330.158826092742100
2.3814-2.62090.20141540.161725962750100
2.6209-2.99970.22511450.168826002745100
2.9997-3.77760.20031380.15826472785100
3.7776-26.59120.18721270.15042678280598
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)
17.56764.81452.59915.7891.48754.9763-0.19030.11860.4282-0.0740.05490.14490.1026-0.07230.10160.18120.0088-0.0140.08640.00150.1691-0.711123.108921.2926
25.7341-0.6086-2.92052.89211.42275.19860.29160.18750.6185-0.1424-0.08550.0267-0.6324-0.1571-0.17380.28160.05220.03120.21970.00880.2705-29.750314.22627.3392
39.0177-2.7707-4.79144.15052.22386.85-0.136-0.483-0.16280.14470.16590.0276-0.0630.1674-0.020.1403-0.0263-0.01330.1263-0.00450.1596-21.69935.806530.2421
41.6543-0.1101-0.0622.4590.99622.3896-0.0110.07720.060.0477-0.0034-0.06120.1398-0.04970.01420.1212-0.01010.00220.08110.01630.10940.147424.475822.1076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:17)A0 - 17
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:67)A18 - 67
3X-RAY DIFFRACTION3chain 'A' and (resseq 68:87)A68 - 87
4X-RAY DIFFRACTION4chain 'A' and (resseq 88:226)A88 - 226

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