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- PDB-2uvd: The crystal structure of a 3-oxoacyl-(acyl carrier protein) reduc... -

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Basic information

Entry
Database: PDB / ID: 2uvd
TitleThe crystal structure of a 3-oxoacyl-(acyl carrier protein) reductase from Bacillus anthracis (BA3989)
Components3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
KeywordsOXIDOREDUCTASE / 3-OXOACYL-(ACYL CARRIER PROTEIN) REDUCTASE / BETA-KETOACYL-(ACYL CARRIER PROTEIN) REDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE (SDR) / OXFORD PROTEIN PRODUCTION FACILITY / NADP / FABG / OPPF / LIPID SYNTHESIS / STRUCTURAL PROTEOMICS IN EUROPE (SPINE) / STRUCTURAL GENOMICS / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / NAD binding / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / : / PKS_KR / 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
3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesBACILLUS ANTHRACIS (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZaccai, N.R. / Carter, L.G. / Berrow, N.S. / Sainsbury, S. / Nettleship, J.E. / Walter, T.S. / Harlos, K. / Owens, R.J. / Wilson, K.S. / Stuart, D.I. ...Zaccai, N.R. / Carter, L.G. / Berrow, N.S. / Sainsbury, S. / Nettleship, J.E. / Walter, T.S. / Harlos, K. / Owens, R.J. / Wilson, K.S. / Stuart, D.I. / Esnouf, R.M. / Oxford Protein Production Facility (OPPF) / Structural Proteomics in Europe (SPINE)
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2008
Title: Crystal Structure of a 3-Oxoacyl-(Acylcarrier Protein) Reductase (Ba3989) from Bacillus Anthracis at 2.4-A Resolution.
Authors: Zaccai, N.R. / Carter, L.G. / Berrow, N.S. / Sainsbury, S. / Nettleship, J.E. / Walter, T.S. / Harlos, K. / Owens, R.J. / Wilson, K.S. / Stuart, D.I. / Esnouf, R.M.
History
DepositionMar 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 24, 2017Group: Structure summary
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
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_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: 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
E: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
F: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
G: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
H: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE


Theoretical massNumber of molelcules
Total (without water)209,2568
Polymers209,2568
Non-polymers00
Water10,359575
1
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


Theoretical massNumber of molelcules
Total (without water)104,6284
Polymers104,6284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13000 Å2
ΔGint-93.7 kcal/mol
Surface area44290 Å2
MethodPQS
2
E: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
F: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
G: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE
H: 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE


Theoretical massNumber of molelcules
Total (without water)104,6284
Polymers104,6284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-116.5 kcal/mol
Surface area44080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.620, 120.650, 136.380
Angle α, β, γ (deg.)90.00, 104.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAAA2 - 362 - 36
21LEULEUALAALABB2 - 362 - 36
31LEULEUALAALACC2 - 362 - 36
41LEULEUALAALADD2 - 362 - 36
51LEULEUALAALAEE2 - 362 - 36
61LEULEUALAALAFF2 - 362 - 36
71LEULEUALAALAGG2 - 362 - 36
81LEULEUALAALAHH2 - 362 - 36
12LYSLYSVALVALAA41 - 5941 - 59
22LYSLYSVALVALBB41 - 5941 - 59
32LYSLYSVALVALCC41 - 5941 - 59
42LYSLYSVALVALDD41 - 5941 - 59
52LYSLYSVALVALEE41 - 5941 - 59
62LYSLYSVALVALFF41 - 5941 - 59
72LYSLYSVALVALGG41 - 5941 - 59
82LYSLYSVALVALHH41 - 5941 - 59
13VALVALALAALAAA63 - 6663 - 66
23VALVALALAALABB63 - 6663 - 66
33VALVALALAALACC63 - 6663 - 66
43VALVALALAALADD63 - 6663 - 66
53VALVALALAALAEE63 - 6663 - 66
63VALVALALAALAFF63 - 6663 - 66
73VALVALALAALAGG63 - 6663 - 66
83VALVALALAALAHH63 - 6663 - 66
14ASPASPTHRTHRAA68 - 7068 - 70
24ASPASPTHRTHRBB68 - 7068 - 70
34ASPASPTHRTHRCC68 - 7068 - 70
44ASPASPTHRTHRDD68 - 7068 - 70
54ASPASPTHRTHREE68 - 7068 - 70
64ASPASPTHRTHRFF68 - 7068 - 70
74ASPASPTHRTHRGG68 - 7068 - 70
84ASPASPTHRTHRHH68 - 7068 - 70
15METMETLEULEUAA72 - 9872 - 98
25METMETLEULEUBB72 - 9872 - 98
35METMETLEULEUCC72 - 9872 - 98
45METMETLEULEUDD72 - 9872 - 98
55METMETLEULEUEE72 - 9872 - 98
65METMETLEULEUFF72 - 9872 - 98
75METMETLEULEUGG72 - 9872 - 98
85METMETLEULEUHH72 - 9872 - 98
16METMETVALVALAA101 - 124101 - 124
26METMETVALVALBB101 - 124101 - 124
36METMETVALVALCC101 - 124101 - 124
46METMETVALVALDD101 - 124101 - 124
56METMETVALVALEE101 - 124101 - 124
66METMETVALVALFF101 - 124101 - 124
76METMETVALVALGG101 - 124101 - 124
86METMETVALVALHH101 - 124101 - 124
17METMETLEULEUAA128 - 172128 - 172
27METMETLEULEUBB128 - 172128 - 172
37METMETLEULEUCC128 - 172128 - 172
47METMETLEULEUDD128 - 172128 - 172
57METMETLEULEUEE128 - 172128 - 172
67METMETLEULEUFF128 - 172128 - 172
77METMETLEULEUGG128 - 172128 - 172
87METMETLEULEUHH128 - 172128 - 172
18ILEILEALAALAAA177 - 188177 - 188
28ILEILEALAALABB177 - 188177 - 188
38ILEILEALAALACC177 - 188177 - 188
48ILEILEALAALADD177 - 188177 - 188
58ILEILEALAALAEE177 - 188177 - 188
68ILEILEALAALAFF177 - 188177 - 188
78ILEILEALAALAGG177 - 188177 - 188
88ILEILEALAALAHH177 - 188177 - 188
19LEULEUALAALAAA204 - 219204 - 219
29LEULEUALAALABB204 - 219204 - 219
39LEULEUALAALACC204 - 219204 - 219
49LEULEUALAALADD204 - 219204 - 219
59LEULEUALAALAEE204 - 219204 - 219
69LEULEUALAALAFF204 - 219204 - 219
79LEULEUALAALAGG204 - 219204 - 219
89LEULEUALAALAHH204 - 219204 - 219
110ALAALAVALVALAA221 - 245221 - 245
210ALAALAVALVALBB221 - 245221 - 245
310ALAALAVALVALCC221 - 245221 - 245
410ALAALAVALVALDD221 - 245221 - 245
510ALAALAVALVALEE221 - 245221 - 245
610ALAALAVALVALFF221 - 245221 - 245
710ALAALAVALVALGG221 - 245221 - 245
810ALAALAVALVALHH221 - 245221 - 245

NCS oper:
IDCodeMatrixVector
1given(-0.93814, 0.23725, 0.2522), (0.24607, -0.05561, 0.96765), (0.2436, 0.96986, -0.00621)32.275, -31.075, 22.29
2given(-0.19925, -0.79471, 0.57336), (-0.78999, -0.21594, -0.57383), (0.57984, -0.56728, -0.58479)-1.965, -11.003, -11.919
3given(0.15715, 0.55015, -0.82015), (0.54577, -0.74051, -0.39215), (-0.82307, -0.38598, -0.41663)28.416, -42.705, 11.671
4given(-0.97921, -0.19686, -0.04897), (0.04646, 0.01734, -0.99877), (0.19747, -0.98028, -0.00783)53.482, 34.802, 20.066
5given(0.98263, -0.05032, -0.17863), (-0.04321, -0.99812, 0.04347), (-0.18048, -0.035, -0.98296)-5.521, -1.11, 68.768
6given(0.28027, -0.53824, 0.79482), (0.6457, 0.7184, 0.25881), (-0.7103, 0.44068, 0.54888)-28.85, -72.151, -12.895
7given(-0.28424, 0.77964, -0.558), (-0.65918, 0.2637, 0.70423), (0.69619, 0.568, 0.43897)39.956, -46.215, -54.575

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Components

#1: Protein
3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE / 3-OXOACYL-ACYL CARRIER PROTEIN REDUCTASE


Mass: 26157.039 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS ANTHRACIS (anthrax bacterium) / Strain: AMES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q81JG6, UniProt: A0A6L7H0J7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 52 %
Crystal growpH: 7
Details: HAMPTON INDEX CONDITION 88: POLYETHYLENE GLYCOL 3350 20 % (W/V) AND 0.2 M TRI-AMMONIUM CITRATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 82223 / % possible obs: 94.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.6 / % possible all: 64.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q7C

1q7c


Resolution: 2.4→27.77 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.483 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4130 5.1 %RANDOM
Rwork0.18 ---
obs0.182 77199 94 %-
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: 47.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å22.07 Å2
2---1.52 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14624 0 0 575 15199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214744
X-RAY DIFFRACTIONr_bond_other_d0.0050.029544
X-RAY DIFFRACTIONr_angle_refined_deg1.341.95219928
X-RAY DIFFRACTIONr_angle_other_deg1.358323560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40251960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31326.053608
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.975152656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1481572
X-RAY DIFFRACTIONr_chiral_restr0.0960.22424
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022656
X-RAY DIFFRACTIONr_nbd_refined0.2070.23180
X-RAY DIFFRACTIONr_nbd_other0.2030.29963
X-RAY DIFFRACTIONr_nbtor_refined0.1670.27416
X-RAY DIFFRACTIONr_nbtor_other0.0890.28215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2481
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4070.259
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4260.2159
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3820.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.725512700
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.2271015552
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.884105654
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.132204376
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2529 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.030.05
8Htight positional0.030.05
1Atight thermal3.0610
2Btight thermal3.3210
3Ctight thermal3.3310
4Dtight thermal3.3310
5Etight thermal3.4210
6Ftight thermal3.2710
7Gtight thermal3.4610
8Htight thermal3.3110
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 175
Rwork0.263 3687

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