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- PDB-4ol9: Crystal Structure of putative 2-dehydropantoate 2-reductase PanE ... -

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Basic information

Entry
Database: PDB / ID: 4ol9
TitleCrystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate
ComponentsPutative 2-dehydropantoate 2-reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ketopantoate reductase
Function / homology
Function and homology information


2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase activity / pantothenate biosynthetic process / NADP binding / cytosol
Similarity search - Function
Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain ...Ketopantoate reductase ApbA/PanE / Ketopantoate reductase, C-terminal domain / Ketopantoate reductase PanE/ApbA C terminal / Ketopantoate reductase, N-terminal domain / Ketopantoate reductase PanE/ApbA / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / OXAMIC ACID / 2-dehydropantoate 2-reductase / 2-dehydropantoate 2-reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of putative 2-dehydropantoate 2-reductase PanE from Mycobacterium tuberculosis complexed with NADP and oxamate
Authors: Dranow, D.M. / Wernimont, A.K. / Abendroth, A. / Pierce, P.G. / Bullen, J. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
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_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_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: Putative 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2326
Polymers32,2131
Non-polymers1,0195
Water5,098283
1
A: Putative 2-dehydropantoate 2-reductase
hetero molecules

A: Putative 2-dehydropantoate 2-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,46412
Polymers64,4262
Non-polymers2,03810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6870 Å2
ΔGint-24 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.590, 108.520, 47.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-674-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative 2-dehydropantoate 2-reductase / / Ketopantoate reductase / KPA reductase / KPR


Mass: 32212.980 Da / Num. of mol.: 1 / Fragment: MytuD.18678.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2573, MT2649, MTCY227.28c / Production host: Escherichia coli (E. coli)
References: UniProt: Q50648, UniProt: P9WIL1*PLUS, 2-dehydropantoate 2-reductase

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Non-polymers , 6 types, 288 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-OXM / OXAMIC ACID / Oxamic acid


Mass: 89.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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.: 283 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein incubated with 4mM NADP for ~5min, then added 1 to 1 with Morpheus(g5): 10% PEG-20,0000, 20% PEG-MME-550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each sodium formate, ammonium acetate, ...Details: Protein incubated with 4mM NADP for ~5min, then added 1 to 1 with Morpheus(g5): 10% PEG-20,0000, 20% PEG-MME-550, 0.1M MOPS/HEPES-Na, pH=7.5, 0.02M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartarate, sodium oxamate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.85→55.5 Å / Num. all: 29148 / Num. obs: 29066 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 25.385 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.5373.4113966214699.9
1.9-1.950.4364.28132852051100
1.95-2.010.3435.27129531998100
2.01-2.070.2796.44126291944100
2.07-2.140.2257.7812360190799.9
2.14-2.210.1918.97119201834100
2.21-2.290.1819.8411442178199.8
2.29-2.390.14611.7311051170799.8
2.39-2.490.12413.410759165899.9
2.49-2.620.11414.6610049155799.9
2.62-2.760.116.289733150999.9
2.76-2.930.08718.429092142099.6
2.93-3.130.0721.568460133499.9
3.13-3.380.0625.247904126899.5
3.38-3.70.05528.526959114099.1
3.7-4.140.04930.216305103999
4.14-4.780.04631.45563395499.4
4.78-5.850.04430.3486480699.1
5.85-8.270.04229.67382163298.6
8.270.03333.55207338197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G17

3g17


Resolution: 1.85→55.5 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.1665 / WRfactor Rwork: 0.1342 / FOM work R set: 0.8908 / SU B: 3.973 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1053 / SU Rfree: 0.1011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1765 1475 5.1 %RANDOM
Rwork0.1458 ---
obs0.1473 29066 99.7 %-
all-30541 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.15 Å2 / Biso mean: 20.119 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20 Å2
2---1.04 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.85→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 65 283 2518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192315
X-RAY DIFFRACTIONr_bond_other_d0.0010.022236
X-RAY DIFFRACTIONr_angle_refined_deg1.4962.0013181
X-RAY DIFFRACTIONr_angle_other_deg0.78835111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.115304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65722.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44715333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02505
X-RAY DIFFRACTIONr_mcbond_it0.8221.1231208
X-RAY DIFFRACTIONr_mcbond_other0.8221.1211206
X-RAY DIFFRACTIONr_mcangle_it1.3851.6761514
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 123 -
Rwork0.194 2017 -
all-2140 -
obs--99.72 %
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)
11.2968-0.1548-0.17621.2013-0.26811.2408-0.02130.0831-0.0433-0.0804-0.0024-0.0861-0.00780.0780.02370.0479-0.01660.01910.06250.00120.041956.726216.2592-11.3791
21.2911-0.05550.07750.5445-0.16841.1429-0.0338-0.0567-0.06480.00780.0076-0.07850.01760.01110.02620.0513-0.0088-0.00460.04170.00240.058754.152415.274-1.2615
30.46530.2299-0.18910.4228-0.20670.32790.0206-0.07440.00870.0037-0.03840.0212-0.05370.04170.01780.0718-0.0119-0.00850.0688-0.00110.05343.280417.02349.195
40.64990.01290.05680.72260.12170.7325-0.04160.0023-0.05560.0133-0.0006-0.06020.0050.00980.04220.0545-0.0102-0.0030.05710.00590.049639.78976.78017.588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 87
2X-RAY DIFFRACTION2A88 - 140
3X-RAY DIFFRACTION3A141 - 225
4X-RAY DIFFRACTION4A226 - 295

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