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- PDB-7kxa: Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH... -

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Basic information

Entry
Database: PDB / ID: 7kxa
TitleCrystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii in complex with NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / Mycobacterium kansasii / InhA / Enoyl-[acyl-carrier-protein] reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium kansasii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of Enoyl-[acyl-carrier-protein] reductase [NADH] (InhA) from Mycobacterium kansasii in complex with NAD
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7565
Polymers29,8961
Non-polymers8604
Water4,738263
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,02320
Polymers119,5854
Non-polymers3,43816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Buried area21320 Å2
ΔGint-145 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.670, 97.670, 141.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-462-

HOH

21A-506-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29896.293 Da / Num. of mol.: 1 / Fragment: MykaA.00472.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium kansasii (bacteria) / Gene: inhA, BZL29_3124, BZL30_8369 / Plasmid: MykaA.00472.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1V3XDT0, UniProt: X7XQY2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 267 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.26 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: RigakuReagents JCSG+ screen C9: 25% (V/V) propanediol-1,2, 10% (V/V) glycerol, 100mM potassium phosphate monobasic / sodium phosphate dibasic pH 6.5: MykaA.00472.a.B1.PS38576 at 27.08mg/ml + ...Details: RigakuReagents JCSG+ screen C9: 25% (V/V) propanediol-1,2, 10% (V/V) glycerol, 100mM potassium phosphate monobasic / sodium phosphate dibasic pH 6.5: MykaA.00472.a.B1.PS38576 at 27.08mg/ml + 4.5mM NAD: tray 318760 c9: cryo: 20% EG: puck nso5-4.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 12, 2020 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 37516 / % possible obs: 99.9 % / Redundancy: 10.439 % / Biso Wilson estimate: 34.693 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.057 / Χ2: 0.954 / Net I/σ(I): 23.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.855.6350.6262.2927160.8660.6999.3
1.85-1.96.8150.5183.1826390.9220.561100
1.9-1.958.640.4014.825880.9630.426100
1.95-2.0110.2820.3196.6224960.980.335100
2.01-2.0811.6130.2439.4424440.9870.25499.9
2.08-2.1511.7940.19511.6223540.9920.204100
2.15-2.2311.7410.14515.5322860.9950.151100
2.23-2.3211.7410.1171922000.9970.122100
2.32-2.4311.730.09922.7821070.9990.104100
2.43-2.5511.7010.08525.4320240.9980.089100
2.55-2.6811.6440.07130.3919330.9990.074100
2.68-2.8511.610.0634.8718350.9980.063100
2.85-3.0411.50.05339.917430.9990.055100
3.04-3.2911.3820.04645.2316240.9990.048100
3.29-3.611.2220.04150.1815020.9990.043100
3.6-4.0311.0730.03753.9513780.9980.03899.9
4.03-4.6510.9850.03355.5212200.9990.035100
4.65-5.6910.9510.03156.41106110.03299.9
5.69-8.0510.590.02754.5484710.028100
8.05-508.9340.02551.655190.9990.02697.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19rc4-4035refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 6udf, apo structure

6udf


Resolution: 1.8→33.87 Å / SU ML: 0.168 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9494
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1696 1962 5.24 %0
Rwork0.1509 35480 --
obs0.1519 37442 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2014 0 54 263 2331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092147
X-RAY DIFFRACTIONf_angle_d0.9362929
X-RAY DIFFRACTIONf_chiral_restr0.0611333
X-RAY DIFFRACTIONf_plane_restr0.0114399
X-RAY DIFFRACTIONf_dihedral_angle_d12.7191814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.27351380.2252474X-RAY DIFFRACTION99.28
1.85-1.890.26181390.19982470X-RAY DIFFRACTION99.92
1.89-1.950.20631260.18182516X-RAY DIFFRACTION99.89
1.95-2.010.22321200.17162494X-RAY DIFFRACTION99.96
2.01-2.090.20831480.16472484X-RAY DIFFRACTION99.92
2.09-2.170.19111570.16242497X-RAY DIFFRACTION99.96
2.17-2.270.19371590.14752464X-RAY DIFFRACTION99.96
2.27-2.390.18491420.15142514X-RAY DIFFRACTION99.96
2.39-2.540.1761410.15272506X-RAY DIFFRACTION100
2.54-2.730.18411360.15492541X-RAY DIFFRACTION100
2.73-3.010.16561200.14982579X-RAY DIFFRACTION100
3.01-3.440.16691300.14772573X-RAY DIFFRACTION100
3.44-4.330.13021570.12712596X-RAY DIFFRACTION99.96
4.34-33.870.15711490.15132772X-RAY DIFFRACTION99.59
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)
11.93573756205-0.1509803810340.6552350468462.73223569021-0.4915992857781.68610733026-0.0247564948384-0.121075919116-0.04393261962510.0539864785244-0.10317451246-0.342768572353-0.0827854895910.4263370551450.08920226686020.126698262872-0.00245464720024-0.004754028608460.4114857412790.0722909554760.2462865483558.44176222593-39.986387682-16.5966508402
23.08383605639-0.0450625638296-0.6805860293241.20985706847-0.1050708478432.045125827120.0191666681430.3818936745610.176767428024-0.0905117546859-0.13796976659-0.306124233769-0.1649407937680.4685556250030.1172248010580.225489737264-0.0790154468672-0.02148028099940.4849260508060.06579899334790.2900275769910.1880983832-30.5661694962-25.2477624006
33.56261172645-2.64574279879-0.6131908048773.060578385221.338249666991.51771586614-0.151878897199-0.2536889136920.2463784689010.1137876494120.18181559559-0.260404852344-0.1245199523770.378734814599-0.1063018260010.182792550233-0.0637563227354-0.01781953138290.2301812367170.04497122624810.205075529214-5.49790351928-28.687577584-17.7446014877
41.95055577838-0.609084461223-0.4670227001481.244939306720.2109594830391.409260479940.01361948763470.05776986418790.0793534536749-0.0407938036346-0.0602783437397-0.15808072434-0.08894240947270.1969310305220.05200752969870.17249458235-0.0166429168188-0.03607289134410.255105216580.0376571903690.195425326133-7.33309900959-32.2944720306-23.0999450395
51.10806911557-0.318704416651-0.02451393231571.336377026370.1628076898610.146323218322-0.0234481160208-0.06672197117180.1087325029810.02773189018690.0338196347091-0.0306096568102-0.111222451980.1017863490280.0003682021026690.164820070849-0.00174401495516-0.01350221800350.2480049770820.02821586652270.238957882335-9.07605690006-35.1647962788-19.2255419435
61.025372979-2.22527086352-0.8208036908015.419285570431.667667515690.68553406176-0.210148827071-0.3482673921310.07124306930280.5275357584020.262021839252-0.216846359299-0.00274885404978-0.190166633192-0.06590614015710.2910400849890.0808611153157-0.04809092376940.523138652732-0.04497864307150.292029984302-16.1806174554-38.4706281204-1.72390259726
71.12835413364-0.09639174960980.4054258720091.33449162011-0.3902132864462.57564931154-0.0419614132948-0.122156918334-0.004466287585590.0646269012241-0.0702431238549-0.1057488016210.04716240633740.3249956114930.09534254753040.149580519970.0419201469134-0.004328905170610.2113418896280.02696985441940.213987756437-9.0803784705-48.3301954787-16.8986021847
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 53 )2 - 531 - 52
22chain 'A' and (resid 54 through 82 )54 - 8253 - 81
33chain 'A' and (resid 83 through 112 )83 - 11282 - 111
44chain 'A' and (resid 113 through 158 )113 - 158112 - 157
55chain 'A' and (resid 159 through 208 )159 - 208158 - 207
66chain 'A' and (resid 209 through 225 )209 - 225208 - 224
77chain 'A' and (resid 226 through 269 )226 - 269225 - 268

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