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- PDB-4gkb: Crystal structure of a short chain dehydrogenase homolog (target ... -

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Basic information

Entry
Database: PDB / ID: 4gkb
TitleCrystal structure of a short chain dehydrogenase homolog (target efi-505321) from burkholderia multivorans, unliganded structure
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / putative sugar dehydrogenase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


L-fucose dehydrogenase / fucose catabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / nucleotide binding / metal ion 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
L-fucose dehydrogenase / 3-oxoacyl-[acyl-carrier protein] reductase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsVetting, M.W. / Hobbs, M.E. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a short chain dehydrogenase homolog (target efi-505321) from burkholderia multivorans, unliganded structure
Authors: Vetting, M.W. / Hobbs, M.E. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionAug 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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

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)111,36116
Polymers110,8424
Non-polymers51912
Water19,2761070
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17720 Å2
ΔGint-148 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.960, 99.960, 205.801
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] reductase / Short-chain dehydrogenase/reductase SDR


Mass: 27710.441 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Strain: ATCC 17616 / Gene: BMULJ_04919, Bmul_3598, fabG / Plasmid: pET30 / Production host: Escherichia coli (E. coli)
References: UniProt: A9ANE0, UniProt: A0A0H3KNE7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7.5
Details: Protein (50 mM Hepes pH 7.5; Reservoir (0.2 M Calcium Acetate 0.1 M HEPES:NaOH pH 7.5 10% (w/v) PEG 8000); Cryoprotection (Reservoir, + 20% Ethylene glycol), sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→86.567 Å / Num. all: 185302 / Num. obs: 185302 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.589.30.8360.9250791270850.836100
1.58-1.689.10.5771.3231426255630.577100
1.68-1.798.80.3931.9211896240460.393100
1.79-1.948.60.2592.3191965223580.259100
1.94-2.128.40.1733.4172862206290.173100
2.12-2.378.30.1433.9154083186120.143100
2.37-2.748.40.1264.8137914164350.126100
2.74-3.3590.0866.7125181139150.086100
3.35-4.7410.40.05411.3111845107700.054100
4.74-22.87311.40.04313.76698658890.04399.1

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDE

1yde


Resolution: 1.5→22.873 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.9063 / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 16.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1719 9297 5.02 %RANDOM
Rwork0.1513 ---
all0.1524 185136 --
obs0.1524 185136 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63 Å2 / Biso mean: 15.9898 Å2 / Biso min: 3.19 Å2
Refinement stepCycle: LAST / Resolution: 1.5→22.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7639 0 21 1070 8730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077942
X-RAY DIFFRACTIONf_angle_d1.08710849
X-RAY DIFFRACTIONf_chiral_restr0.0761246
X-RAY DIFFRACTIONf_plane_restr0.0051432
X-RAY DIFFRACTIONf_dihedral_angle_d13.8342837
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5-1.5170.24943370.233559196256
1.517-1.53490.25422980.21758536151
1.5349-1.55360.21473230.208857776100
1.5536-1.57330.22583240.198659006224
1.5733-1.5940.23812890.192558206109
1.594-1.61580.21383360.1958036139
1.6158-1.63890.22113230.175558976220
1.6389-1.66330.19923090.175258126121
1.6633-1.68930.23460.166657966142
1.6893-1.7170.20122920.167358906182
1.717-1.74660.2013040.169358576161
1.7466-1.77830.20342810.166258736154
1.7783-1.81250.18752900.160359136203
1.8125-1.84950.19682880.153458636151
1.8495-1.88970.15983050.147658476152
1.8897-1.93360.15833080.148958336141
1.9336-1.9820.16273070.145558546161
1.982-2.03550.17752980.142958946192
2.0355-2.09540.17473060.145158626168
2.0954-2.1630.14332830.133658926175
2.163-2.24020.16552980.136558586156
2.2402-2.32980.17033120.141258876199
2.3298-2.43580.16753250.141158426167
2.4358-2.5640.1663280.14658586186
2.564-2.72440.16343180.150558376155
2.7244-2.93440.16523090.146258856194
2.9344-3.22890.1563020.147558656167
3.2289-3.69450.15643180.139758726190
3.6945-4.64820.14473220.1358616183
4.6482-22.87570.17493180.158859196237
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)
11.0982-0.28190.14460.6936-0.09240.7353-0.02750.20610.1141-0.151-0.02880.1333-0.1322-0.0898-0.01690.10360.0452-0.07420.1916-0.00110.1205-46.934632.1003-24.8831
20.3466-0.11840.07870.09280.09760.57790.05140.11660.1595-0.2004-0.08070.1737-0.2996-0.18740.24390.05770.0815-0.10180.1625-0.00750.1437-48.328938.9863-12.9
30.90650.05480.03320.25810.16640.551-0.01160.04650.1748-0.1214-0.02490.0845-0.112-0.041-0.02680.05920.0078-0.02460.07480.00750.0683-33.052533.0916-14.3039
41.2939-0.0283-0.03050.40510.31840.95060.01970.1691-0.1588-0.0996-0.05740.06850.1444-0.04080.01880.0812-0.0023-0.00280.0847-0.02460.0613-27.53269.697-22.8145
50.4063-0.1182-0.00370.3284-0.04890.64440.01770.0478-0.0662-0.0641-0.0548-0.01880.11260.03450.0310.05140.0020.00860.05460.00140.0516-19.077511.4136-11.5628
60.39210.6524-0.49411.1338-0.73840.7717-0.0911-0.0181-0.1803-0.1054-0.0527-0.07550.31940.01440.07410.1494-0.00520.02330.09270.01020.1183-33.07047.0796-5.6783
70.7203-0.7882-0.10533.0255-1.60881.5137-0.0079-0.1425-0.10860.14610.0280.08650.1542-0.0541-0.00910.0978-0.0481-0.0160.11370.00720.0966-44.28947.9872-0.6436
80.29240.0455-0.1380.3027-0.00580.3761-0.0131-0.0072-0.014-0.0348-0.03680.04850.0177-0.07070.02550.0298-0.0034-0.01440.0804-0.00380.054-34.046320.8089-10.4782
90.7833-0.1220.37831.0271-0.15470.5513-0.0396-0.18390.10780.18320.0039-0.1368-0.08450.1004-0.01680.0955-0.0348-0.0350.1467-0.01470.0766-11.367428.421523.6766
100.3906-0.2181-0.05510.4457-0.07850.3504-0.0323-0.1368-0.01150.1031-0.0201-0.1046-0.03570.1724-0.00690.0438-0.0241-0.02270.10470.02250.056-11.324919.873312.7344
110.5660.1849-0.35130.2969-0.22060.5531-0.0379-0.0634-0.0179-0.0869-0.0643-0.20680.03030.27620.02980.0696-0.03980.01490.18150.00940.1188-10.979335.95515.2712
120.29880.103-0.06460.339-0.11740.41490.0025-0.06760.05930.0274-0.0288-0.0079-0.08580.01920.01760.0546-0.01870.00080.0723-0.01430.0591-22.453733.845910.8202
130.2368-0.1413-0.05090.36260.00870.44790.012-0.12130.14630.0526-0.04750.0563-0.1617-0.1210.01060.09220.01650.00390.1084-0.05980.1333-40.297846.637915.366
140.2795-0.04870.11450.67940.11420.53430.0165-0.09890.10520.077-0.05470.24730.005-0.1319-0.0330.0533-0.01650.0150.098-0.03360.0926-35.71231.988614.5356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 43 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 170 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 171 through 258 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 43 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 44 through 174 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 175 through 200 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 201 through 220 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 221 through 258 )B0
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 43 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 44 through 170 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 171 through 220 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 221 through 258 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 170 )D0
14X-RAY DIFFRACTION14chain 'D' and (resid 171 through 258 )D0

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