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

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Basic information

Entry
Database: PDB / ID: 4gvx
TitleCrystal structure of a short chain dehydrogenase homolog (target EFI-505321) from burkholderia multivorans, with bound NADP and L-fucose
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 / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 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
beta-L-fucopyranose / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-fucose dehydrogenase / 3-oxoacyl-[acyl-carrier protein] reductase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 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, with bound NADP and L-fucose
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 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)115,07324
Polymers110,8424
Non-polymers4,23120
Water18,6281034
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

A: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,03524
Polymers110,8424
Non-polymers4,19320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area24840 Å2
ΔGint-92 kcal/mol
Surface area30010 Å2
MethodPISA
2
B: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

B: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,11024
Polymers110,8424
Non-polymers4,26920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area25100 Å2
ΔGint-86 kcal/mol
Surface area30360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.437, 118.522, 118.283
Angle α, β, γ (deg.)90.000, 92.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-435-

HOH

21B-653-

HOH

31C-432-

HOH

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#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 / Production host: Escherichia coli (E. coli)
References: UniProt: A9ANE0, UniProt: A0A0H3KNE7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase
#4: Sugar
ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1050 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1034 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (50 mM Hepes pH 7.5, 5 mM NADP + 25 mM L-Fucose; Reservoir (0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% Peg8000); Cryoprotection (Reservoir + 20% Ethylene glycol + 5 mM NADP + 25 mM L-FUCOSE) ...Details: Protein (50 mM Hepes pH 7.5, 5 mM NADP + 25 mM L-Fucose; Reservoir (0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% Peg8000); Cryoprotection (Reservoir + 20% Ethylene glycol + 5 mM NADP + 25 mM L-FUCOSE), VAPOR DIFFUSION, SITTING DROP, 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 MX225HE / Detector: CCD / Date: Aug 13, 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→100 Å / Num. all: 145388 / Num. obs: 145388 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.103 / Χ2: 1.21 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.532.70.49473870.88198.7
1.53-1.552.70.42874610.822199
1.55-1.582.70.37173590.804198.9
1.58-1.622.70.33873670.821198.7
1.62-1.652.70.30774280.816198.6
1.65-1.692.70.28173820.826198.5
1.69-1.732.70.25373380.854198.3
1.73-1.782.80.21573770.799198.2
1.78-1.832.80.273360.823197.9
1.83-1.892.80.18773530.847197.7
1.89-1.962.80.17173030.938197
1.96-2.042.80.14372900.956197.5
2.04-2.132.80.14472721.299196.7
2.13-2.242.80.13672511.735196.7
2.24-2.382.80.13772372.239196.1
2.38-2.562.80.12171662.397195.7
2.56-2.822.90.171952.222195
2.82-3.232.90.05770871.351194.2
3.23-4.072.90.04270381.478193
4.07-1002.90.03167611.125188.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GLO

4glo


Resolution: 1.499→28.74 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.909 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 16.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1792 7293 5.02 %RANDOM
Rwork0.152 ---
obs0.1533 145306 96.6 %-
all-145306 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.57 Å2 / Biso mean: 11.0002 Å2 / Biso min: 1.87 Å2
Refinement stepCycle: LAST / Resolution: 1.499→28.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 269 1034 9103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068360
X-RAY DIFFRACTIONf_angle_d1.16611431
X-RAY DIFFRACTIONf_chiral_restr0.0791316
X-RAY DIFFRACTIONf_plane_restr0.0051476
X-RAY DIFFRACTIONf_dihedral_angle_d14.9982993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4988-1.51580.22712480.20314560480896
1.5158-1.53370.21472490.20064607485698
1.5337-1.55240.23032420.19014748499099
1.5524-1.5720.20822640.18494625488999
1.572-1.59270.20562470.17744745499299
1.5927-1.61450.21762350.1724650488599
1.6145-1.63760.21632540.17324682493698
1.6376-1.6620.2252340.17094705493999
1.662-1.6880.1812620.16314666492898
1.688-1.71570.18252490.16384659490898
1.7157-1.74520.20482590.16644695495499
1.7452-1.7770.19142490.16034611486098
1.777-1.81110.1932460.1614683492998
1.8111-1.84810.2032200.15864699491998
1.8481-1.88830.17672550.15234600485598
1.8883-1.93220.17472310.154602483397
1.9322-1.98050.17252500.15054621487197
1.9805-2.0340.16052450.14544663490897
2.034-2.09390.192340.14854589482397
2.0939-2.16140.17912730.14734573484697
2.1614-2.23870.1632400.14234611485197
2.2387-2.32830.16792010.14424615481696
2.3283-2.43420.16572530.14494550480396
2.4342-2.56240.1832160.14944573478996
2.5624-2.72290.17372340.14934555478995
2.7229-2.93290.18722660.1474497476395
2.9329-3.22770.18982320.15114516474894
3.2277-3.69390.14372520.13034452470494
3.6939-4.65070.15032280.13094398462691
4.6507-28.74550.17562250.1524263448888
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)
10.550.10830.06210.34790.08860.9959-0.00920.00580.07370.05950.0208-0.0036-0.1786-0.001-0.02180.04760.00130.01760.0279-0.00660.04391.5128-50.250614.9015
20.30210.03450.00821.7052-0.95690.9773-0.0277-0.01970.04530.1799-0.0031-0.0946-0.11170.0582-0.00050.0964-0.00530.00570.0519-0.0160.06524.0684-47.366322.035
30.3883-0.0073-0.09140.44360.10740.27490.0128-0.0230.00210.072-0.00210.0403-0.0115-0.0135-0.01910.0266-0.00080.0120.02580.00170.0337-1.6729-66.329919.3844
40.35240.0888-0.16920.3241-0.00990.5032-0.0292-0.0376-0.02480.09030.0353-0.1231-0.00070.1577-0.00380.00780.00340.00360.0721-0.01430.085716.7702-65.70939.7933
50.166-0.08580.00740.3311-0.05660.1780.009-0.0161-0.0023-0.04310.0186-0.0192-0.0410.0167-0.02440.0286-0.00260.00960.0362-0.00140.04143.906-63.44122.4897
60.45380.02440.12730.80970.16370.30660.01910.08380.0072-0.2042-0.06920.00610.03650.01610.02790.12660.027-0.00140.0684-0.00690.0371-3.1509-31.98432.5968
70.46240.1657-0.25210.7381-0.57711.3510.02180.05990.0056-0.04940.00380.02620.145-0.04860.00970.11290.011-0.01690.0535-0.01980.0523-6.5234-39.360330.1891
80.4243-0.0740.07510.38770.03810.57130.03870.023-0.0283-0.0339-0.03160.0010.13460.03060.00410.08360.0136-0.00740.0459-0.00260.038-1.7593-37.165548.8238
91.8880.0856-0.05640.76520.08260.64380.001-0.0948-0.0855-0.0504-0.03950.09170.0686-0.07310.01840.06720.0014-0.01080.0615-0.00220.0389-10.0937-30.115347.1256
101.72030.8459-0.70231.5413-0.31631.47210.0107-0.0923-0.1599-0.0668-0.01710.28860.0523-0.2191-0.01230.0348-0.0001-0.02380.1223-0.01140.1385-24.5698-21.65847.7299
110.27080.04520.02910.2489-0.06120.419-0.00080.01210.0047-0.061-0.01620.0138-0.0271-0.0190.02080.05350.0098-0.00660.0511-0.0030.0358-5.8073-19.935345.6228
120.45760.0943-0.06770.218-0.02210.96030.03730.0228-0.07790.04740.06170.02130.1769-0.00730.03830.0587-0.0003-0.0020.03450.02550.0692-2.45-102.63615.002
130.3197-0.2357-0.1190.83720.29480.4248-0.0086-0.0103-0.0930.14140.03180.08680.083-0.0404-0.01980.0825-0.00610.00290.05690.0240.0804-5.25-104.44122.478
140.4529-0.24940.09310.514-0.08440.3302-0.0058-0.0767-0.02670.10180.01680.00020.02490.0174-0.00410.0454-0.00140.00040.03720.01560.04631.271-88.94523.653
150.9851-0.82020.47721.3984-0.37350.44910.03990.00760.0472-0.0261-0.0224-0.00430.01660.02340.00280.0175-0.00690.00650.0360.00850.0504-4.308-83.7711.785
160.3524-0.1232-0.16510.52450.07020.54150.01730.0054-0.00760.0504-0.0088-0.06410.00840.0371-0.00840.01630.00060.00150.02910.00250.03995.095-82.67913.556
171.39140.07630.02440.4449-0.04080.7072-0.0065-0.02620.08620.07080.04740.11490.0447-0.14070.00210.033-0.00570.01840.04370.02020.0716-13.567-87.66512.857
180.577-0.495-0.40711.08070.25260.89710.007-0.15910.06120.0360.00490.2374-0.013-0.31340.0038-0.0222-0.00890.01990.12560.00880.1605-21.901-86.9634.045
190.2244-0.0559-0.01290.31650.03810.1908-0.0076-0.0103-0.0483-0.02390.01890.03150.0173-0.0099-0.00280.0297-0.00420.00120.03210.00250.0514-4.047-89.5152.37
200.56040.02690.00580.5188-0.30140.4029-0.02970.1321-0.0425-0.1559-0.04640.0021-0.13160.09360.01110.161-0.0065-0.00790.05560.02950.01850.647-2.19933.081
210.33820.07610.19780.57550.53741.1205-0.00910.0992-0.0043-0.0386-0.0632-0.053-0.10190.1320.01140.18660.00290.01150.09810.02660.05253.7185.2831.53
220.27-0.01090.05960.3347-0.05210.4765-0.01640.01320.043-0.0494-0.0127-0.0016-0.1659-0.01980.01950.11190.0058-0.01180.04640.00560.0357-3.9732.08648.752
231.93660.3040.24190.77520.06670.5405-0.0636-0.035-0.0074-0.0180.0001-0.189-0.14470.1450.01570.0835-0.024-0.00620.08530.01370.06110.926-4.2448.735
241.11610.76960.44251.82090.29881.308-0.0322-0.06580.09050.00850.0097-0.3030.00630.2223-0.02910.038-0.0051-0.00670.13910.00540.108219.36-12.92349.944
250.29690.02440.03160.27310.04410.4295-0.01890.0178-0.0061-0.059-0.0178-0.02650.00540.02370.02760.05690.0057-0.00130.03880.00290.03311.743-14.8646.265
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 66 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 174 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 175 through 220 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 258 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 43 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 44 through 66 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 67 through 170 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 171 through 200 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 201 through 220 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 221 through 258 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 43 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 44 through 66 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 67 through 131 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 132 through 150 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 151 through 174 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 175 through 200 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 201 through 220 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 221 through 258 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 43 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 44 through 66 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 67 through 174 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 175 through 200 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 201 through 220 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 221 through 258 )D0

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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