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- PDB-6otu: Crystal structure of a glucose-6-phosphate isomerase from Chlamyd... -

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Basic information

Entry
Database: PDB / ID: 6otu
TitleCrystal structure of a glucose-6-phosphate isomerase from Chlamydia trachomatis D/UW-3/Cx
ComponentsGlucose-6-phosphate isomerase
KeywordsISOMERASE / NIAID / sexually transmitted infection / STI / National Institute of Allergy and Infectious Diseases / glucoe-6-phosphate / fructose-6-phosphate / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glucose-6-phosphate isomerase / glucose-6-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
Similarity search - Function
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUCOSE-6-PHOSPHATE / Glucose-6-phosphate isomerase
Similarity search - Component
Biological speciesChlamydia trachomatis D/UW-3/CX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a glucose-6-phosphate isomerase from Chlamydia trachomatis D/UW-3/Cx
Authors: Edwards, T.E. / Dranow, D.M. / Horanyi, P.S. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionMay 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2255
Polymers58,7881
Non-polymers4374
Water3,531196
1
A: Glucose-6-phosphate isomerase
hetero molecules

A: Glucose-6-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,45010
Polymers117,5752
Non-polymers8758
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/21
Buried area14140 Å2
ΔGint-80 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.660, 95.660, 124.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

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Components

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


Mass: 58787.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis D/UW-3/CX (bacteria)
Gene: pgi_1, pgi, pgi_2, pgi_4, ERS095036_01728, ERS133246_04369, ERS133248_01345
Variant: D/UW-3/Cx / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E9E8R5, glucose-6-phosphate isomerase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#3: Chemical ChemComp-G6Q / GLUCOSE-6-PHOSPHATE / Glucose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ChtrB.17127.a.B1.PW38523 at 18.94 mg/mL with 3 mM glucose-6-phosphate against MCSG3 screen condition C11 0.1 M Tris pH 8.5, 0.2 M ammonium acetate, 45% MPD, crystal tracking ID 305213c11, unique puck ID lyz8-7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→44.647 Å / Num. obs: 26976 / % possible obs: 95.9 % / Redundancy: 10.051 % / Biso Wilson estimate: 41.791 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.105 / Χ2: 1.017 / Net I/σ(I): 16.25 / Num. measured all: 271137 / Scaling rejects: 62
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.3110.1560.5993.4520261204519950.8760.63197.6
2.31-2.3710.1570.5723.8519440196719140.8930.60397.3
2.37-2.4410.1750.4694.4219220194118890.9350.49497.3
2.44-2.5210.2180.3895.4818729188018330.9480.40997.5
2.52-2.610.2470.3496.1718157182817720.960.36796.9
2.6-2.6910.2120.2917.3817391175517030.9710.30697
2.69-2.7910.2610.238917053171916620.980.2596.7
2.79-2.910.1750.19710.6216300166116020.9870.20796.4
2.9-3.0310.1820.15713.4915426157515150.9910.16696.2
3.03-3.1810.1560.13215.8314929152614700.9940.13996.3
3.18-3.3510.1440.10120.0813948144213750.9960.10695.4
3.35-3.569.9790.08323.9213282139513310.9970.08795.4
3.56-3.89.9710.06628.812225128912260.9980.06995.1
3.8-4.119.8490.05932.3511326121011500.9980.06295
4.11-4.59.6680.05136.710277113110630.9970.05394
4.5-5.039.7510.04738.3938010249620.9990.04993.9
5.03-5.819.70.04736.4583139188570.9990.0593.4
5.81-7.129.7770.04437.4372067957370.9990.04792.7
7.12-10.069.4260.03543.9154016265730.9990.03791.5
10.06-44.6478.280.03242.6428733963470.9990.03487.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.15_3459refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bzb

6bzb


Resolution: 2.25→44.647 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2214 1494 5.89 %
Rwork0.1562 --
obs0.1599 25380 90.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→44.647 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 12 196 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074034
X-RAY DIFFRACTIONf_angle_d0.8985460
X-RAY DIFFRACTIONf_dihedral_angle_d8.0912385
X-RAY DIFFRACTIONf_chiral_restr0.05612
X-RAY DIFFRACTIONf_plane_restr0.006715
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2499-2.32260.34721160.24641942X-RAY DIFFRACTION82
2.3226-2.40560.3071170.24041962X-RAY DIFFRACTION83
2.4056-2.50190.31411580.19792064X-RAY DIFFRACTION89
2.5019-2.61570.25941320.18512108X-RAY DIFFRACTION89
2.6157-2.75360.27831320.17712148X-RAY DIFFRACTION90
2.7536-2.92610.23371380.17742184X-RAY DIFFRACTION92
2.9261-3.1520.2621450.16882227X-RAY DIFFRACTION94
3.152-3.46910.23191200.15482282X-RAY DIFFRACTION94
3.4691-3.97080.17071370.13062282X-RAY DIFFRACTION94
3.9708-5.00170.1831400.1152304X-RAY DIFFRACTION94
5.0017-44.65540.18841590.15022383X-RAY DIFFRACTION92
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)
10.52810.3206-0.36912.46660.14491.5752-0.08880.11890.0242-0.29550.07740.0880.0966-0.01860.01790.37730.15-0.04610.3972-0.01050.24156.850417.286611.7103
27.46782.70812.14153.75990.94252.0193-0.41390.38240.8396-0.68820.15730.3642-0.33320.01780.28760.48390.18730.02660.3460.0560.41915.493747.965611.3654
30.25160.4023-0.1611.06280.0432.0775-0.009-0.06680.0565-0.0626-0.0545-0.01160.00620.16430.07650.37030.16510.01550.348-0.0370.422928.272140.61429.0937
41.15680.07680.09810.5916-0.22550.7406-0.0529-0.09510.25150.02150.064-0.1049-0.2331-0.0660.00840.42480.16360.01090.3752-0.04750.462619.808949.835128.8907
50.35020.1041-0.07140.8139-0.2310.49110.04480.041-0.0127-0.1435-0.0374-0.02990.06110.0699-0.00370.40810.1680.02390.3686-0.01840.301621.468818.378618.6023
60.9914-0.14960.55081.1003-0.45180.61620.02-0.25420.14010.139-0.01860.1267-0.1786-0.23830.01750.40450.16620.01750.4183-0.04550.38498.699331.498933.0812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 140 )
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 190 )
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 278 )
5X-RAY DIFFRACTION5chain 'A' and (resid 279 through 457 )
6X-RAY DIFFRACTION6chain 'A' and (resid 458 through 525 )

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