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- PDB-3zu2: Structure of the enoyl-ACP reductase FabV from Yersinia pestis wi... -

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Basic information

Entry
Database: PDB / ID: 3zu2
TitleStructure of the enoyl-ACP reductase FabV from Yersinia pestis with the cofactor NADH (SIRAS)
ComponentsPUTATIVE REDUCTASE YPO4104/Y4119/YP_4011
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS II / SHORT-CHAIN DEHYDROGENASE REDUCTASE SUPERFAMILY
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsHirschbeck, M.W. / Kuper, J. / Kisker, C.
CitationJournal: Structure / Year: 2012
Title: Structure of the Yersinia Pestis Fabv Enoyl-Acp Reductase and its Interaction with Two 2-Pyridone Inhibitors
Authors: Hirschbeck, M.W. / Kuper, J. / Lu, H. / Liu, N. / Neckles, C. / Shah, S. / Wagner, S. / Sotriffer, C.A. / Tonge, P.J. / Kisker, C.
History
DepositionJul 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: PUTATIVE REDUCTASE YPO4104/Y4119/YP_4011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6103
Polymers45,9221
Non-polymers6882
Water2,882160
1
A: PUTATIVE REDUCTASE YPO4104/Y4119/YP_4011
hetero molecules

A: PUTATIVE REDUCTASE YPO4104/Y4119/YP_4011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2206
Polymers91,8432
Non-polymers1,3774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area5670 Å2
ΔGint-34.4 kcal/mol
Surface area32560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.160, 104.160, 219.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2092-

HOH

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Components

#1: Protein PUTATIVE REDUCTASE YPO4104/Y4119/YP_4011 / ENOYL-ACP REDUCTASE


Mass: 45921.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Strain: CO92 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8Z9U1
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE (NAI): NADH

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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: 4.08 Å3/Da / Density % sol: 69.9 % / Description: NONE
Crystal growDetails: 1.25M SODIUM MALONATE, 100MM IMIDAZOLE PH 8.25.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONBESSY 14.110.918
SYNCHROTRONESRF ID2921.25
Detector
TypeIDDetector
MARRESEARCH1CCD
ADSC CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
21.251
ReflectionResolution: 2.1→39.4 Å / Num. obs: 48035 / % possible obs: 99.8 % / Observed criterion σ(I): 2.5 / Redundancy: 7.2 % / Biso Wilson estimate: 44.83 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.8
Reflection shellRedundancy: 7.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.1→34.821 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 2018 5 %
Rwork0.1994 --
obs0.2009 40073 95.84 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.595 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2821 Å20 Å20 Å2
2---0.2821 Å20 Å2
3---0.5641 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 45 160 3375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073310
X-RAY DIFFRACTIONf_angle_d1.1364497
X-RAY DIFFRACTIONf_dihedral_angle_d16.3261264
X-RAY DIFFRACTIONf_chiral_restr0.073497
X-RAY DIFFRACTIONf_plane_restr0.004584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.17510.33921920.30713529X-RAY DIFFRACTION91
2.1751-2.26210.33251900.29653547X-RAY DIFFRACTION91
2.2621-2.36510.34041980.28733609X-RAY DIFFRACTION93
2.3651-2.48970.30792060.27093663X-RAY DIFFRACTION94
2.4897-2.64560.32261930.26123744X-RAY DIFFRACTION96
2.6456-2.84980.27811680.26283863X-RAY DIFFRACTION97
2.8498-3.13650.27522210.23433900X-RAY DIFFRACTION99
3.1365-3.58990.2372020.20343986X-RAY DIFFRACTION99
3.5899-4.52140.18352290.15484020X-RAY DIFFRACTION100
4.5214-34.82530.17792190.16054194X-RAY DIFFRACTION98
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)
14.44420.2742-3.86163.29571.9514.81140.20581.79780.25450.4139-2.0029-0.1595-1.6121-2.87791.51691.0940.2418-0.02031.3154-0.38641.008532.283692.9212-35.0184
20.88650.0701-0.80680.5872-0.97282.6055-0.26450.0148-0.2274-0.7404-0.4171-0.40841.36780.29370.5680.81970.11320.34650.19960.15680.321431.682477.5379-15.4223
32.29850.041-0.84624.0127-2.65173.9346-0.1124-0.20340.0290.2436-0.11360.01380.0788-0.77530.14630.3205-0.1080.04680.42870.04050.268820.909474.68178.1886
40.1590.00170.11874.3679-1.45562.8249-0.05820.0155-0.01070.0019-0.5312-0.78940.1859-0.10890.46040.3344-0.04560.04750.33050.18160.477832.034178.02078.4406
50.22670.77090.01215.3128-0.70071.90180.0174-0.06850.13720.356-0.6594-2.0515-0.12360.42390.66790.3259-0.0549-0.08290.37360.40450.973143.104776.970414.6129
60.08820.48890.05316.06790.50050.2197-0.16060.8421-0.3313-0.67540.0634-1.71860.24270.80610.18891.41370.16730.66230.30470.10620.924739.700448.0889-2.6041
70.5537-0.007-0.34462.1741-1.18462.0242-0.1789-0.2036-0.28840.584-0.7255-1.68950.47550.47360.88130.5096-0.0405-0.1040.42730.5081.160545.929266.419819.0129
82.146-0.81061.09690.8352-1.90624.8350.116-0.1381-0.7711-1.6143-0.3237-0.89391.77550.22590.28841.2375-0.07450.27810.25590.26450.845136.826250.800611.9343
92.7652-0.2123-1.09960.9374-2.09865.58240.2064-0.2468-0.87620.6485-0.9479-1.23391.04670.34460.64940.642-0.125-0.24190.29310.44340.970942.812462.520425.8525
100.0722-0.05260.22082.3374-2.14582.0839-0.19580.00790.0281-0.4624-0.3882-0.62280.88420.13060.54040.8868-0.15590.20140.32130.16360.466129.957556.85838.1873
110.7360.63710.10472.2595-0.43060.1154-0.1567-0.0959-0.12180.2033-0.07870.32080.3075-0.73960.08870.6791-0.21270.12080.48420.07460.373521.917463.191317.4506
124.58431.58340.47090.75180.89073.1575-0.04060.0196-0.88050.5535-0.5529-0.49310.85870.09990.51540.8573-0.22640.04210.480.2430.528430.115755.589223.6533
135.22346.3001-5.67648.9111-8.60218.8132-1.1318-0.2341-1.5355-2.58760.3629-0.58441.818-0.4180.97191.6296-0.40070.32670.25810.06290.493324.202444.7367.1285
144.21466.40930.99569.55640.97813.06520.2917-0.0682-0.5183-0.4313-0.2397-0.8111.8299-0.74620.01821.4754-0.2030.21020.39940.06530.399324.723156.3727-5.5581
151.12230.87571.2333.9386-1.24725.7743-0.47060.10770.4089-0.684-0.3612-0.3444-0.3629-0.21810.59210.34180.02810.16460.29270.11270.420829.108881.3129-4.0098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:62)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 63:122)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 123:176)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 177:205)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 206:245)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 246:263)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 264:285)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 286:320)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 321:345)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 346:357)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 358:375)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 376:399)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 400:422)

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