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- PDB-4bii: How nature bridges the gap: Crystallographic elucidation of pyrid... -

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Basic information

Entry
Database: PDB / ID: 4bii
TitleHow nature bridges the gap: Crystallographic elucidation of pyridomycin binding to InhA
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
KeywordsOXIDOREDUCTASE / ACP ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyridomycin / Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRead, J.A. / Gingell, H.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Pyridomycin Bridges the Nadh and Substrate Binding Pockets of the Enoyl Reductase Inha
Authors: Hartkoorn, R. / Pojer, F. / Read, J.A. / Gingell, H. / Neres, J. / Horlacher, O. / Altmann, K.H. / Cole, S.
History
DepositionApr 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Feb 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,83110
Polymers114,2194
Non-polymers3,6126
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17400 Å2
ΔGint-120.8 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.852, 110.285, 67.519
Angle α, β, γ (deg.)90.00, 98.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH] / ENOYL-ACYL CARRIER PROTEIN REDUCTASE / NADH-DEPENDENT ENOYL-ACP REDUCTASE


Mass: 28554.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PYW / Pyridomycin


Mass: 540.565 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H32N4O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.09 Å3/Da / Density % sol: 41.21 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: May 12, 2012 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.95→110 Å / Num. obs: 113532 / % possible obs: 88.4 % / Observed criterion σ(I): 1.95 / Redundancy: 3.3 % / Biso Wilson estimate: 24.66 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / % possible all: 44.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→28.55 Å / Cor.coef. Fo:Fc: 0.9411 / Cor.coef. Fo:Fc free: 0.9261 / SU R Cruickshank DPI: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.195 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.154
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.205 3014 5.02 %RANDOM
Rwork0.1778 ---
obs0.1792 60060 87.79 %-
Displacement parametersBiso mean: 26.31 Å2
Baniso -1Baniso -2Baniso -3
1-3.1472 Å20 Å2-0.9964 Å2
2---4.9658 Å20 Å2
3---1.8186 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7439 0 249 410 8098
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017932HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0610842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2606SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1258HARMONIC5
X-RAY DIFFRACTIONt_it7932HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion17.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1085SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9715SEMIHARMONIC4
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2913 67 3.68 %
Rwork0.2929 1752 -
all0.2928 1819 -
obs--87.79 %
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)
10.7906-0.15750.22210.6857-0.02960.8075-0.0224-0.07990.11770.1205-0.00060.0405-0.1706-0.21620.023-0.02270.05460.0214-0.0137-0.0065-0.05630.028713.447228.6245
20.8191-0.33670.00550.64920.10951.02240.01180.0636-0.20130.0011-0.0158-0.07860.23630.00060.004-0.03050.0004-0.001-0.1083-0.01290.055523.5331-19.296411.9973
30.8461-0.24310.10830.70540.12830.8090.04260.2421-0.0345-0.1407-0.0283-0.02-0.0784-0.1448-0.0143-0.04540.02450.00210.03250.0115-0.08735.42012.5454-1.5211
40.6817-0.02370.19350.55690.00320.80770.0128-0.0442-0.01070.1269-0.0255-0.2008-0.06910.10660.0127-0.0507-0.0166-0.0539-0.06490.00440.012629.68593.165634.84
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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