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- PDB-4lgv: X-ray crystal structure of Glucose-6-phosphate 1-dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 4lgv
TitleX-ray crystal structure of Glucose-6-phosphate 1-dehydrogenase from Mycobacterium avium
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / pentose-phosphate shunt / glucose metabolic process / NADP binding
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose-6-phosphate 1-dehydrogenase / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 20, 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 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,93213
Polymers221,4134
Non-polymers5209
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13410 Å2
ΔGint-111 kcal/mol
Surface area66820 Å2
MethodPISA
2
A: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

B: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,93213
Polymers221,4134
Non-polymers5209
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area9450 Å2
ΔGint-90 kcal/mol
Surface area70780 Å2
MethodPISA
3
A: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

B: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,93213
Polymers221,4134
Non-polymers5209
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_564-x+1/2,-y+1,z-1/21
Buried area10190 Å2
ΔGint-92 kcal/mol
Surface area70040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.220, 170.210, 225.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLNGLNAA7 - 46328 - 484
21HISHISGLNGLNBB7 - 46328 - 484
12HISHISGLNGLNAA7 - 46328 - 484
22HISHISGLNGLNCC7 - 46328 - 484
13PROPROPROPROAA8 - 46229 - 483
23PROPROPROPRODD8 - 46229 - 483
14HISHISGLNGLNBB7 - 46328 - 484
24HISHISGLNGLNCC7 - 46328 - 484
15PROPROPROPROBB8 - 46229 - 483
25PROPROPROPRODD8 - 46229 - 483
16PROPROPROPROCC8 - 46229 - 483
26PROPROPROPRODD8 - 46229 - 483

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glucose-6-phosphate 1-dehydrogenase


Mass: 55353.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: zwf, MAV_1252 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QC59, UniProt: A0A0H3A0Q9*PLUS, glucose-6-phosphate dehydrogenase (NADP+)

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Non-polymers , 5 types, 682 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG1 E4: 0.2 M lithium sulfate, 0.1 M TRIS pH 8.50, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.28357 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28357 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 95401 / Num. obs: 94781 / % possible obs: 99.35 % / Redundancy: 5.76 % / Rmerge(I) obs: 0.82 / Net I/σ(I): 17.39

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BH9

2bh9


Resolution: 2.3→19.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.39 / SU B: 11.412 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 4755 5 %RANDOM
Rwork0.1851 ---
obs0.1869 94781 99.35 %-
all-95401 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.25 Å2 / Biso mean: 37.555 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0 Å2-0 Å2
2---0.09 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14112 0 26 673 14811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914545
X-RAY DIFFRACTIONr_bond_other_d0.0080.0213568
X-RAY DIFFRACTIONr_angle_refined_deg1.441.95919844
X-RAY DIFFRACTIONr_angle_other_deg1.231331019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82851826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0223.117709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.916152208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.76815137
X-RAY DIFFRACTIONr_chiral_restr0.0810.22184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02116735
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023448
X-RAY DIFFRACTIONr_mcbond_it1.5642.0677265
X-RAY DIFFRACTIONr_mcbond_other1.5642.0677264
X-RAY DIFFRACTIONr_mcangle_it2.4643.0939074
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A268040.1
12B268040.1
21A273080.09
22C273080.09
31A253380.08
32D253380.08
41B270980.09
42C270980.09
51B249640.1
52D249640.1
61C252040.08
62D252040.08
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 328 -
Rwork0.258 6288 -
all-6616 -
obs--96.37 %
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)
10.47130.02490.43231.9092-0.31451.22510.067-0.0074-0.01010.259-0.0258-0.02940.1165-0.0688-0.04110.2444-0.0136-0.03770.09830.00130.075238.9341123.649242.8086
20.0472-0.0157-0.1621.43220.23490.86640.03470.0143-0.03360.2352-0.0528-0.2562-0.0390.01410.01810.1512-0.0277-0.05990.10640.03980.159642.1802104.666325.7328
30.2912-0.0262-0.00270.85160.1710.26330.01610.02560.06430.0431-0.0179-0.2514-0.0505-0.01560.00180.0762-0.023-0.01510.11350.03840.216946.8833102.506114.1277
41.4397-1.3345-0.09713.92350.12090.1417-0.0342-0.10130.04990.4708-0.0046-0.2713-0.14120.06460.03880.2462-0.0567-0.10370.08910.00440.116142.4004107.232930.9297
51.73460.54351.86452.70151.68162.7444-0.05180.3480.0984-0.15710.2391-0.7568-0.28710.5054-0.18730.165-0.03310.13090.36530.01980.574157.3483106.299510.2774
60.7273-0.09890.02340.7963-0.57031.5509-0.0035-0.0468-0.0211-0.08010.0218-0.02220.2323-0.0495-0.01820.1107-0.0006-0.01450.18560.02620.076527.454366.020756.3279
70.075-0.0471-0.01140.2014-0.1120.8134-0.0171-0.01150.01350.01140.0003-0.00450.0712-0.0530.01680.1252-0.01610.00910.14730.010.121717.696176.506829.3475
80.34860.42150.93232.2621-1.35346.5868-0.0444-0.0241-0.0872-0.20090.0264-0.09070.3645-0.1440.0180.1717-0.00550.08860.0925-0.00720.191422.351163.930310.3522
92.57951.25760.7646.41420.49764.67830.01450.0181-0.15130.26850.1530.03130.38560.1175-0.16750.15910.0138-0.00330.15130.03670.072230.221768.624641.0288
101.1166-0.204-0.15110.3360.01141.6481-0.0154-0.0185-0.0292-0.02980.01120.02850.0421-0.31590.00420.0827-0.0232-0.0050.15630.03590.08989.050375.216326.8114
110.4465-0.0371-0.34710.4525-0.01760.95670.04560.0998-0.02690.0433-0.01940.0198-0.05230.0636-0.02630.1185-0.01120.01550.1909-0.00830.084827.110599.0446-42.8834
120.06010.05930.14520.2117-0.00970.6037-0.0261-0.00360.0038-0.02910.02150.03570.0106-0.02280.00460.1173-0.01480.01230.15670.0110.126117.633296.1179-13.7951
130.5227-0.3643-0.53150.2989-0.0464.8408-0.03960.0270.10980.0436-0.0026-0.0679-0.1934-0.06260.04220.1051-0.0235-0.02850.12510.00940.182725.5267106.95690.6753
140.80730.0913-0.07833.87040.90353.7624-0.0616-0.13670.0955-0.05930.16920.0499-0.10790.3563-0.10760.151-0.01810.00730.19050.00660.06530.7929100.6732-29.9253
151.092-0.36660.8460.7586-0.19661.306-0.027-0.0282-0.0173-0.01470.03140.0641-0.0903-0.2626-0.00440.0658-0.01220.03570.14930.02640.10719.777697.9233-14.5014
160.7739-0.1881-0.07374.039-0.98352.12060.0125-0.0027-0.055-0.19650.07110.19370.28120.0797-0.08370.461300.10450.0265-0.01940.063230.549846.3059-31.9217
170.87260.6084-0.60732.60251.91354.701-0.32080.1429-0.1082-0.4740.1766-0.13630.05210.26430.14420.4585-0.01460.19430.0978-0.00320.104138.616863.8018-28.0283
181.4881-0.051-0.92870.4068-0.24971.6849-0.2111-0.1334-0.2959-0.1249-0.0773-0.14550.43340.07770.28840.2580.07540.14250.06850.04090.212238.963963.7982-5.7404
190.4650.3899-0.15960.5381-0.27771.0155-0.10820.0291-0.1666-0.2104-0.0472-0.28870.28870.19570.15540.19710.12190.12250.12170.00790.213343.962166.6143-4.2036
201.30551.09730.22722.72590.17580.9755-0.17740.0449-0.4202-0.3218-0.0379-0.58010.62090.27290.21530.49380.19370.2710.11410.04470.282543.436961.9458-6.8436
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 144
2X-RAY DIFFRACTION2A145 - 220
3X-RAY DIFFRACTION3A221 - 389
4X-RAY DIFFRACTION4A390 - 430
5X-RAY DIFFRACTION5A431 - 463
6X-RAY DIFFRACTION6B6 - 142
7X-RAY DIFFRACTION7B143 - 342
8X-RAY DIFFRACTION8B343 - 386
9X-RAY DIFFRACTION9B387 - 411
10X-RAY DIFFRACTION10B412 - 463
11X-RAY DIFFRACTION11C7 - 177
12X-RAY DIFFRACTION12C178 - 343
13X-RAY DIFFRACTION13C344 - 387
14X-RAY DIFFRACTION14C388 - 411
15X-RAY DIFFRACTION15C412 - 463
16X-RAY DIFFRACTION16D8 - 144
17X-RAY DIFFRACTION17D145 - 176
18X-RAY DIFFRACTION18D177 - 227
19X-RAY DIFFRACTION19D228 - 369
20X-RAY DIFFRACTION20D370 - 462

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