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- PDB-4eit: Crystal structure of an enoyl-(acyl carrier protein) reductase fr... -

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Basic information

Entry
Database: PDB / ID: 4eit
TitleCrystal structure of an enoyl-(acyl carrier protein) reductase from Bartonella henselae
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / selenomethionine-labeled / acyl-carrier protein / NAD+dependent / fatty acid biosynthesis
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enoyl-[acyl-carrier-protein] reductase [NADH] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of an enoyl-(acyl carrier protein) reductase from Bartonella henselae
Authors: Edwards, T.E. / Craig, T.K. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)180,4576
Polymers180,4576
Non-polymers00
Water3,585199
1
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]


Theoretical massNumber of molelcules
Total (without water)120,3054
Polymers120,3054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15010 Å2
ΔGint-98 kcal/mol
Surface area31050 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]

E: Enoyl-[acyl-carrier-protein] reductase [NADH]
F: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)120,3054
Polymers120,3054
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area15110 Å2
ΔGint-98 kcal/mol
Surface area31050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 76.860, 171.950
Angle α, β, γ (deg.)90.000, 107.990, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYALAALAAA6 - 26110 - 265
21GLYGLYALAALABB6 - 26110 - 265
12GLYGLYLYSLYSAA6 - 26010 - 264
22GLYGLYLYSLYSCC6 - 26010 - 264
13GLYGLYALAALAAA6 - 26110 - 265
23GLYGLYALAALADD6 - 26110 - 265
14GLYGLYLYSLYSAA6 - 26010 - 264
24GLYGLYLYSLYSEE6 - 26010 - 264
15GLYGLYVALVALAA6 - 26210 - 266
25GLYGLYVALVALFF6 - 26210 - 266
16GLYGLYALAALABB4 - 2618 - 265
26GLYGLYALAALACC4 - 2618 - 265
17GLYGLYALAALABB6 - 26110 - 265
27GLYGLYALAALADD6 - 26110 - 265
18ASNASNALAALABB5 - 2619 - 265
28ASNASNALAALAEE5 - 2619 - 265
19GLYGLYALAALABB6 - 26110 - 265
29GLYGLYALAALAFF6 - 26110 - 265
110GLYGLYLYSLYSCC6 - 26010 - 264
210GLYGLYLYSLYSDD6 - 26010 - 264
111ASNASNALAALACC5 - 2619 - 265
211ASNASNALAALAEE5 - 2619 - 265
112GLYGLYLYSLYSCC6 - 26010 - 264
212GLYGLYLYSLYSFF6 - 26010 - 264
113GLYGLYALAALADD6 - 26110 - 265
213GLYGLYALAALAEE6 - 26110 - 265
114GLYGLYLYSLYSDD6 - 26010 - 264
214GLYGLYLYSLYSFF6 - 26010 - 264
115GLYGLYALAALAEE6 - 26110 - 265
215GLYGLYALAALAFF6 - 26110 - 265

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 30076.152 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: BH04310, fabI2, fabl2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6G4D5, UniProt: A0A0H3M2Q2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ...Details: BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 232038b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07806 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07806 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 59634 / Num. obs: 59084 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 44.808 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 10.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.4-2.460.4413.1416632429298.6
2.46-2.530.3993.4516215418298.7
2.53-2.60.3274.1516047414098.7
2.6-2.680.284.7515498400998.9
2.68-2.770.245.4715096389698.9
2.77-2.870.2056.3114350370698.9
2.87-2.980.1557.9414069364299
2.98-3.10.148.813358346699.3
3.1-3.240.11610.1712973337999.1
3.24-3.390.09712.0412282320999.3
3.39-3.580.08113.9511615305099.3
3.58-3.790.07615.211090291699.2
3.79-4.060.06517.0710296272499.5
4.06-4.380.06218.619500253599.5
4.38-4.80.06119.198957237899.5
4.8-5.370.05719.067979211199.8
5.37-6.20.06118.627084188199.2
6.2-7.590.05819.526021161099.6
7.59-10.730.05421.654658126199.8
10.730.0520.88238369796.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.83 Å
Translation2.5 Å47.83 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3grk

3grk


Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.2279 / WRfactor Rwork: 0.1971 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8647 / SU B: 14.653 / SU ML: 0.166 / SU R Cruickshank DPI: 0.4758 / SU Rfree: 0.2474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.476 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 2994 5.1 %RANDOM
Rwork0.1956 ---
obs0.1972 59083 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.87 Å2 / Biso mean: 37.2283 Å2 / Biso min: 11.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-1.21 Å2
2--0.79 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10961 0 0 199 11160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01911185
X-RAY DIFFRACTIONr_bond_other_d0.0070.027039
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.96815214
X-RAY DIFFRACTIONr_angle_other_deg1.349317223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55451489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69123.904415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.094151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2161547
X-RAY DIFFRACTIONr_chiral_restr0.0820.21794
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212716
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022299
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms
11A74650.06
12B74650.06
21A75870.06
22C75870.06
31A74630.07
32D74630.07
41A74970.07
42E74970.07
51A74980.05
52F74980.05
61B77550.07
62C77550.07
71B75730.08
72D75730.08
81B75970.06
82E75970.06
91B75980.04
92F75980.04
101C77080.07
102D77080.07
111C77330.07
112E77330.07
121C76750.06
122F76750.06
131D79970.06
132E79970.06
141D76640.07
142F76640.07
151E76800.05
152F76800.05
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 226 -
Rwork0.265 3932 -
all-4158 -
obs--98.65 %
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)
10.5622-0.10650.5270.2553-0.21080.5715-0.28110.24320.17480.00610.07150.0271-0.26120.18780.20950.2468-0.1906-0.10790.15990.10460.1493-29.918230.1173-39.9279
20.7226-0.01420.58830.292-0.37370.96380.08850.0785-0.1591-0.01570.01620.01280.12530.08-0.10470.1817-0.02860.01870.0913-0.00940.0915-23.8677-7.842-22.7535
30.5518-0.22810.68850.1158-0.25930.8892-0.16380.16390.11120.1043-0.0415-0.0042-0.19480.22470.20520.1708-0.1182-0.00240.19190.0680.115-10.44718.0093-17.3219
40.7206-0.17130.33560.1961-0.35070.6345-0.0296-0.05550.0176-0.05310.05430.01480.1166-0.1309-0.02470.1414-0.12820.0190.1477-0.01350.0677-49.75739.0707-32.1176
50.37390.2549-0.35870.261-0.08640.92440.1273-0.00530.06270.0376-0.06560.0496-0.1025-0.1162-0.06170.09320.03120.01770.16580.00010.1176-49.451417.9843-75.5537
60.6356-0.0301-0.17790.0518-0.08610.62170.0422-0.0696-0.06770.0221-0.00550.02050.1597-0.0715-0.03670.1348-0.0672-0.0220.14140.03510.1115-44.7729-11.1587-69.589
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 262
2X-RAY DIFFRACTION2B4 - 261
3X-RAY DIFFRACTION3C4 - 261
4X-RAY DIFFRACTION4D6 - 261
5X-RAY DIFFRACTION5E5 - 261
6X-RAY DIFFRACTION6F6 - 262

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