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- PDB-4m8s: Crystal structure of 3-ketoacyl -(acyl carrier protein) reductase... -

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Basic information

Entry
Database: PDB / ID: 4m8s
TitleCrystal structure of 3-ketoacyl -(acyl carrier protein) reductase (FabG) from Neisseria meningitidis
ComponentsPutative 3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / FabG / Neisseria / acyl carrier protein / Rossmann Fold / Reductase
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: To be Published
Title: The crystal structure of 3-ketoacyl -(acyl carrier protein) reductase (FabG) from Neisseria meningitidis
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 3-oxoacyl-[acyl-carrier protein] reductase
B: Putative 3-oxoacyl-[acyl-carrier protein] reductase
C: Putative 3-oxoacyl-[acyl-carrier protein] reductase
D: Putative 3-oxoacyl-[acyl-carrier protein] reductase


Theoretical massNumber of molelcules
Total (without water)104,3754
Polymers104,3754
Non-polymers00
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-77 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.890, 111.270, 117.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRMETMETAA3 - 2473 - 247
21THRTHRMETMETBB3 - 2473 - 247
12SERSERPROPROAA2 - 2482 - 248
22SERSERPROPROCC2 - 2482 - 248
13SERSERPROPROAA2 - 2482 - 248
23SERSERPROPRODD2 - 2482 - 248
14THRTHRMETMETBB3 - 2473 - 247
24THRTHRMETMETCC3 - 2473 - 247
15THRTHRPROPROBB3 - 2483 - 248
25THRTHRPROPRODD3 - 2483 - 248
16SERSERPROPROCC2 - 2482 - 248
26SERSERPROPRODD2 - 2482 - 248

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Putative 3-oxoacyl-[acyl-carrier protein] reductase


Mass: 26093.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: FAM18 / Gene: fabG, NMC0302 / Production host: Escherichia coli (E. coli)
References: UniProt: A1KRY4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 41.08 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop
Details: 250mM Ammonium phosphate dibasic, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2013
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→35.36 Å / Num. all: 59818 / Num. obs: 59818 / % possible obs: 100 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.05199.9
8.94-35.36198.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.54 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.451 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19881 3020 5.1 %RANDOM
Rwork0.17324 ---
obs0.17453 56732 99.94 %-
all-56766 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.575 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 0 677 7844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197221
X-RAY DIFFRACTIONr_bond_other_d0.0050.027146
X-RAY DIFFRACTIONr_angle_refined_deg1.1891.9579735
X-RAY DIFFRACTIONr_angle_other_deg1.213316349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025970
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23124.564287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.418151269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6951554
X-RAY DIFFRACTIONr_chiral_restr0.0630.21153
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028347
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021575
X-RAY DIFFRACTIONr_mcbond_it1.1761.7723898
X-RAY DIFFRACTIONr_mcbond_other1.1751.7723897
X-RAY DIFFRACTIONr_mcangle_it2.0542.654862
X-RAY DIFFRACTIONr_mcangle_other2.0542.654863
X-RAY DIFFRACTIONr_scbond_it1.4622.0963323
X-RAY DIFFRACTIONr_scbond_other1.4612.0963324
X-RAY DIFFRACTIONr_scangle_other2.5593.0344874
X-RAY DIFFRACTIONr_long_range_B_refined5.69315.7088805
X-RAY DIFFRACTIONr_long_range_B_other5.45415.1758490
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A138900.13
12B138900.13
21A140940.13
22C140940.13
31A136540.11
32D136540.11
41B136720.13
42C136720.13
51B132180.13
52D132180.13
61C136300.11
62D136300.11
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 225 -
Rwork0.204 4101 -
obs--99.88 %
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)
10.22530.05270.10920.20170.01870.18940.02830.0579-0.0575-0.0158-0.0058-0.0103-0.02860.013-0.02250.04720.00820.01390.0277-0.01320.0413-57.1303125.4734129.0389
20.165-0.0470.09020.09030.07030.2214-0.0327-0.0172-0.0214-0.0273-0.00120.0208-0.0573-0.00110.03390.04660.00390.00340.01220.00260.0475-67.3751151.3392142.526
30.2604-0.01320.19340.19770.13590.2525-0.02280.0271-0.0558-0.00140.0756-0.0112-0.02250.0697-0.05280.00740.00870.01550.06480.00690.0467-32.1764127.7794146.4971
40.1884-0.21960.00070.26820.01170.1232-0.0677-0.0545-0.00960.07230.04850.00950.00360.02890.01930.04430.010.01040.07010.00880.0062-48.0736146.0246165.3661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 248
2X-RAY DIFFRACTION2B3 - 248
3X-RAY DIFFRACTION3C2 - 248
4X-RAY DIFFRACTION4D2 - 248

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