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- PDB-1o5i: Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 1o5i
TitleCrystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution
Components3-oxoacyl-(acyl carrier protein) reductase
KeywordsOXIDOREDUCTASE / TM1169 / 3-OXOACYL-(ACYL CARRIER PROTEIN) REDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / NADP binding
Similarity search - Function
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-oxoacyl-(Acyl carrier protein) reductase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-(acyl carrier protein) reductase
B: 3-oxoacyl-(acyl carrier protein) reductase
C: 3-oxoacyl-(acyl carrier protein) reductase
D: 3-oxoacyl-(acyl carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4085
Polymers110,7444
Non-polymers6631
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-124 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.515, 117.120, 140.847
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
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVALAA4 - 5316 - 65
21GLYGLYVALVALBB4 - 5316 - 65
31GLYGLYVALVALCC4 - 5316 - 65
41GLYGLYVALVALDD4 - 5316 - 65
52LEULEUPHEPHEAA62 - 23574 - 247
62LEULEUPHEPHEBB62 - 23574 - 247
72LEULEUPHEPHECC62 - 23574 - 247
82LEULEUPHEPHEDD62 - 23574 - 247

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Components

#1: Protein
3-oxoacyl-(acyl carrier protein) reductase


Mass: 27686.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1169 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0Q1, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.54 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 20% PEG-6000, 0.1M citric acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.972386
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 10, 2002 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972386 Å / Relative weight: 1
ReflectionResolution: 2.5→41.17 Å / Num. all: 31633 / Num. obs: 31633 / % possible obs: 85.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 51.32 Å2 / Rsym value: 0.12 / Net I/σ(I): 7.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 2231 / Rsym value: 0.229 / % possible all: 42.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: 1i01

1i01


Resolution: 2.5→41.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.212 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.807 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER ...Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER SUBUNITS, ELECTRON DENSITY IS SUGGESTIVE BUT TOO WEAKTO JUSTIFY FITTING NAD, PRESUMABLY DUE TO DIFFERING CRYSTAL CONTACTS. 3. THE DISULFIDE BOND (37-54) HAS NEGATIVE DIFFERENCE DENSITY IN ALL SUBUNITS, PRESUMABLY DUE TO RADIATION DAMAGE. 4. NCS IS BROKEN AT RESIDUES 54-61 AND 84/137, DUE TO CRYSTAL CONTACTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1562 4.9 %RANDOM
Rwork0.19404 ---
obs0.19662 30035 85.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20 Å20 Å2
2---6.16 Å20 Å2
3---8.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7165 0 35 161 7361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227310
X-RAY DIFFRACTIONr_bond_other_d0.0020.026956
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9789890
X-RAY DIFFRACTIONr_angle_other_deg0.944316116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7475932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36523.916286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.263151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7951551
X-RAY DIFFRACTIONr_chiral_restr0.0950.21165
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028033
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021432
X-RAY DIFFRACTIONr_nbd_refined0.2040.21602
X-RAY DIFFRACTIONr_nbd_other0.1890.27081
X-RAY DIFFRACTIONr_nbtor_other0.0890.24713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0310.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4870.23
X-RAY DIFFRACTIONr_mcbond_it0.7051.54752
X-RAY DIFFRACTIONr_mcangle_it1.21627474
X-RAY DIFFRACTIONr_scbond_it1.64832868
X-RAY DIFFRACTIONr_scangle_it2.7744.52416
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1319tight positional0.060.05
2B1319tight positional0.060.05
3C1319tight positional0.060.05
4D1319tight positional0.050.05
1A2000loose positional0.525
2B2000loose positional0.485
3C2000loose positional0.595
4D2000loose positional0.545
1A1319tight thermal1.6710
2B1319tight thermal1.9610
3C1319tight thermal2.3110
4D1319tight thermal2.1310
1A2000loose thermal1.8510
2B2000loose thermal2.1610
3C2000loose thermal2.5210
4D2000loose thermal2.3910
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 50 5.08 %
Rwork0.264 934 -
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)
10.65360.34850.28431.2601-0.07431.26980.0175-0.15560.03760.10720.00670.3121-0.1512-0.1895-0.0242-0.09330.02060.03790.0293-0.01-0.148334.64844.61852.406
21.20380.07840.10821.6167-0.01180.86560.0567-0.0729-0.04370.0821-0.0324-0.39820.11260.2763-0.0243-0.10840.0316-0.02750.0430.0031-0.118555.06422.51450.516
30.56980.07140.14561.5526-0.32791.0997-0.03560.1516-0.3752-0.4691-0.03920.00930.25150.01530.07490.14560.03870.0670.0569-0.0515-0.091546.35720.20120.705
41.4537-0.62730.18911.2104-0.39151.09520.07590.19560.1654-0.3849-0.1266-0.1779-0.20780.12850.05060.08990.01350.02610.00310.0195-0.203240.58149.922.232
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 4 - 237 / Label seq-ID: 16 - 249

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD

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