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- PDB-3hjb: 1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase f... -

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Basic information

Entry
Database: PDB / ID: 3hjb
Title1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / glucose-6-phosphate isomerase / pgi / idp01329 / Gluconeogenesis / Glycolysis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / glucose 6-phosphate metabolic process / monosaccharide binding / gluconeogenesis / glycolytic process / cytosol
Similarity search - Function
Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. ...Phosphoglucose isomerase, C-terminal domain / Phosphoglucose isomerase, C-terminal domain - #10 / Phosphoglucose isomerase, C-terminal / Phosphoglucose isomerase signature 1. / Phosphoglucose isomerase (PGI) / Phosphoglucose isomerase, conserved site / Phosphoglucose isomerase, SIS domain 1 / Phosphoglucose isomerase, SIS domain 2 / Phosphoglucose isomerase / Phosphoglucose isomerase signature 2. / Glucose-6-phosphate isomerase family profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.5 Angstrom Crystal Structure of Glucose-6-phosphate Isomerase from Vibrio cholerae.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,75048
Polymers253,5694
Non-polymers2,18144
Water73,3394071
1
A: Glucose-6-phosphate isomerase
B: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,84425
Polymers126,7842
Non-polymers1,06023
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-235 kcal/mol
Surface area35830 Å2
MethodPISA
2
C: Glucose-6-phosphate isomerase
D: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,90623
Polymers126,7842
Non-polymers1,12121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-218 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.661, 75.094, 127.456
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucose-6-phosphate isomerase / GPI / Phosphoglucose isomerase / PGI / Phosphohexose isomerase / PHI


Mass: 63392.148 Da / Num. of mol.: 4 / Mutation: M179V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: pgi, VC_0374 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9KUY4, glucose-6-phosphate isomerase

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Non-polymers , 6 types, 4115 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4071 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein solution: 7.7 mg/mL protein, 0.01M Tris-HCl, 0.25M Sodium Cloride, Screen solution (PACT II, drop B11): 0.2M Calcium chloride, 0.1M MES pH 6.0, 25% w/v PEG 6000., VAPOR DIFFUSION, ...Details: Protein solution: 7.7 mg/mL protein, 0.01M Tris-HCl, 0.25M Sodium Cloride, Screen solution (PACT II, drop B11): 0.2M Calcium chloride, 0.1M MES pH 6.0, 25% w/v PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 370201 / Num. obs: 370201 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.4 / Num. unique all: 16052 / % possible all: 85

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0044refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GZD

1gzd


Resolution: 1.5→29.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.905 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1507 18596 5 %RANDOM
Rwork0.12653 ---
all0.12774 351339 --
obs0.12774 351339 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å2-0.04 Å2
2--0.28 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17164 0 92 4071 21327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218786
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212238
X-RAY DIFFRACTIONr_angle_refined_deg1.371.92725663
X-RAY DIFFRACTIONr_angle_other_deg0.909330059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.76152443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60525.276906
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.827153063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7011557
X-RAY DIFFRACTIONr_chiral_restr0.1020.22781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023851
X-RAY DIFFRACTIONr_mcbond_it0.9541.511654
X-RAY DIFFRACTIONr_mcbond_other0.3211.54725
X-RAY DIFFRACTIONr_mcangle_it1.62218856
X-RAY DIFFRACTIONr_scbond_it2.62337132
X-RAY DIFFRACTIONr_scangle_it4.2774.56794
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 1306 -
Rwork0.184 23057 -
obs-23057 87.44 %
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)
10.4750.248-0.18220.5824-0.13860.7499-0.03770.0298-0.0629-0.05160.0166-0.06660.0960.07020.02110.0320.02360.00210.0276-0.00580.044651.0965-32.9736.03
20.3867-0.0901-0.01990.57660.08430.59830.0094-0.05250.07140.06680.001-0.0323-0.10460.0656-0.01050.0472-0.0185-0.00420.0207-0.01080.017849.9832-4.820256.3448
31.4958-0.4782.29880.4413-1.5847.41970.03590.0123-0.0840.0740.05870.10250.0432-0.3269-0.09460.1138-0.01630.0270.0498-0.01010.102935.3132-2.897854.7387
40.98040.14720.70450.61540.14081.5445-0.0242-0.00410.16720.0216-0.00370.0361-0.1597-0.0520.02790.07850.01130.00840.0067-0.00630.061636.32877.768749.4766
51.3357-0.9978-0.37541.88430.35160.55280.02930.02640.2581-0.03830.0211-0.2339-0.13460.0891-0.05040.0966-0.02910.00210.0317-0.01090.092850.46458.409850.5372
60.3250.0577-0.03360.2788-0.0050.40270.0106-0.0045-0.01050.01120.0064-0.00590.01820.0071-0.0170.00820.0038-0.00230.002-0.00070.001440.3599-23.964844.285
710.41890.89-1.64333.39410.04022.89110.2177-0.3424-0.63450.1603-0.1644-0.08220.1906-0.1646-0.05330.1035-0.0625-0.0380.04910.0310.089913.816-49.770542.3251
80.48330.0915-0.01380.2631-0.04960.3160.00460.0079-0.0287-0.00240.01040.02420.0459-0.012-0.01490.01250.0007-0.0010.00170.00120.006638.1665-27.926440.633
93.8177-4.8345-0.6038.27211.4231.92810.01550.02940.4681-0.09740.0827-0.4853-0.22890.1235-0.09820.0476-0.00720.02070.01630.01420.079137.76644.928225.9851
101.65530.4644-0.14441.86090.09372.16750.07670.07150.2405-0.0221-0.00740.0027-0.3502-0.1371-0.06930.09030.04290.02440.02930.02850.057923.64237.246723.1585
110.35220.0226-0.28150.49890.01470.5232-0.01450.0979-0.0208-0.07730.01730.01860.0259-0.1154-0.00280.02870.004-0.0160.08290.00690.023214.9018-18.821720.103
121.36980.19040.48681.20290.75292.4118-0.0002-0.0493-0.06480.0539-0.05730.14310.0826-0.28290.05750.01530.01430.01370.08190.01380.0567-3.4222-14.110847.9464
130.5647-0.0987-0.16090.4643-0.20841.31420.0227-0.0570.06030.0810.0058-0.0051-0.1272-0.0407-0.02850.02760.01180.00640.0316-0.00340.014913.8032-8.518757.514
142.8872-2.9014-1.42535.69033.23212.24180.1410.056-0.0115-0.1205-0.0138-0.1793-0.1617-0.0134-0.12720.05540.00510.00820.05350.01240.052219.5126-13.881956.2289
152.279-1.5371-0.3641.412-0.02180.6424-0.0005-0.0879-0.07450.01970.0460.0530.0157-0.0169-0.04540.02480.0019-0.00110.02990.00950.010617.8799-20.592363.138
160.5854-0.13720.8710.24960.16783.85210.0599-0.1526-0.12740.0639-0.00360.04560.2373-0.2724-0.05630.0545-0.01120.0090.09420.02810.05655.6068-22.094363.8025
170.2419-0.0605-0.19190.23640.13030.38810.01870.05490.0229-0.01320.00640.0143-0.0231-0.088-0.02510.00480.0090.00150.03360.01090.00514.3771-14.074835.0053
180.55060.1561-0.0810.224-0.06340.31880.00130.05610.02070.00330.0119-0.0342-0.0313-0.0158-0.01320.00970.00710.00190.01180.0040.01129.5916-11.437728.2708
191.6089-0.14623.19551.259-0.736410.1740.0057-0.2198-0.062-0.0010.02550.07390.3021-0.5404-0.03120.0246-0.01040.00570.03440.00890.017523.4025-39.962952.7282
201.5279-0.0353-0.34931.81640.28152.8961-0.0251-0.1081-0.0830.14450.003-0.03810.2405-0.03430.02210.07120.0091-0.00240.01280.00770.01437.0211-41.712458.7711
211.5368-0.481.24391.3086-0.56931.7028-0.1116-0.12340.10670.12090.0368-0.0138-0.1768-0.17860.07480.06170.0240.01770.0837-0.01510.023579.55525.190648.6474
220.4872-0.15530.32660.6435-0.01070.48770.0019-0.09620.00470.06470.01460.01960.0164-0.1206-0.01650.0241-0.01250.01670.07830.01190.022577.565810.66542.6827
231.10880.0201-0.20621.07340.60282.1374-0.0080.03810.0457-0.0388-0.06340.1438-0.058-0.26330.07140.0109-0.0118-0.01140.07560.01390.044860.23679.856616.2406
240.57010.05390.17820.5042-0.28161.30560.02330.0494-0.063-0.07280.0011-0.0050.1246-0.0115-0.02450.0237-0.0125-0.00330.0313-0.00480.017377.07864.10256.4067
251.68451.15210.53240.8020.46381.0650.0146-0.0029-0.11140.0083-0.0078-0.06690.0515-0.0057-0.00680.03270.0068-0.00850.0212-0.00020.034487.456113.46644.9118
262.31611.36640.05662.23830.01081.27380.01060.08440.1559-0.03590.03210.0524-0.07060.0106-0.04270.0174-0.0044-0.00110.03920.01330.016879.318216.51790.1528
271.16540.2609-1.01280.69420.16424.16490.05020.16880.1687-0.06760.02630.0892-0.2302-0.284-0.07650.02950.0078-0.00910.07610.02840.035169.242417.1943-1.7634
280.3220.08790.21150.23150.12460.42290.0071-0.0504-0.00940.00880.00750.01880.0158-0.0815-0.01460.0037-0.0072-0.00050.03170.00930.004677.20310.040228.2792
290.5148-0.12470.08820.2007-0.06570.34570.0039-0.0481-0.0214-0.00010.0106-0.03350.0316-0.0145-0.01450.014-0.0086-0.00050.01290.00270.01292.27467.268334.9904
300.99250.119-0.07161.119-0.1311.5954-0.01960.09620.0822-0.08850.02770.0353-0.1554-0.0973-0.00810.07180.0019-0.00080.01540.01050.020595.437536.76366.9523
310.7918-0.51570.4320.8265-0.32041.0818-0.0705-0.0650.06830.09340.0512-0.0369-0.186-0.00140.01930.0776-0.0322-0.00060.0337-0.01650.0762110.405434.455430.5957
320.3379-0.17120.02380.37910.1030.5547-0.00430.02120.00160.00980.0163-0.08190.04510.1343-0.0120.01450.00090.00420.0454-0.00050.0375120.383714.684519.5772
330.4745-0.0667-0.21071.17550.01180.76320.00710.0716-0.0779-0.1575-0.01210.04680.1115-0.00470.0050.05070.0018-0.01060.0165-0.01570.0173103.9529-2.30543.8542
341.0464-0.015-0.82050.7288-0.00271.5709-0.0105-0.0066-0.13-0.0256-0.00530.02010.1082-0.05110.01580.0616-0.0082-0.0060.0081-0.00410.046699.4498-9.978914.3834
351.45031.05150.39912.18440.60431.0340.0426-0.0115-0.27260.03640.0028-0.18830.2160.0752-0.04550.09860.02490.00030.0124-0.00580.0778111.0481-14.648712.2858
360.3107-0.06970.02940.2489-0.00510.36040.01340.00940.0082-0.01720.0075-0.0104-0.0150.0143-0.02090.0073-0.00310.00330.0022-0.00150.0022103.95819.178519.3628
3710.0983-3.19140.52462.90010.01672.61660.29090.46120.5182-0.1999-0.2129-0.0853-0.1761-0.1328-0.0780.08060.04810.0360.040.03410.071277.49744.915221.3374
380.4634-0.12340.01060.3272-0.05170.31960.00270.00150.03090.00050.00920.0242-0.0516-0.008-0.01190.0114-0.00020.00260.00110.00080.0062101.267323.933922.6332
394.53226.04320.89159.99611.00311.3724-0.0056-0.0267-0.49710.07680.0922-0.59590.20610.114-0.08660.05360.0235-0.00490.02680.0160.0698100.9079-8.620237.3452
402.7843-0.21710.65032.7610.41652.67630.082-0.0241-0.33290.02110.0269-0.02180.36-0.0714-0.10890.0941-0.0402-0.02210.0330.0220.059186.6277-11.99940.5582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 97
2X-RAY DIFFRACTION2A98 - 177
3X-RAY DIFFRACTION3A178 - 182
4X-RAY DIFFRACTION4A183 - 234
5X-RAY DIFFRACTION5A235 - 266
6X-RAY DIFFRACTION6A267 - 436
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