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- PDB-4g81: Crystal structure of a hexonate dehydrogenase ortholog (target ef... -

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Basic information

Entry
Database: PDB / ID: 4g81
TitleCrystal structure of a hexonate dehydrogenase ortholog (target efi-506402 from salmonella enterica, unliganded structure
ComponentsPutative hexonate dehydrogenase
KeywordsOXIDOREDUCTASE / enzyme function initiative / EFI / Structural Genomics / dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Oxidoreductase UcpA / Putative hexonate dehydrogenase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Enteritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVetting, M.W. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a hexonate dehydrogenase ortholog (target efi-506402 from salmonella enterica, unliganded structure
Authors: Vetting, M.W. / Wichelecki, D. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: Putative hexonate dehydrogenase
A: Putative hexonate dehydrogenase
B: Putative hexonate dehydrogenase
C: Putative hexonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,86311
Polymers109,5054
Non-polymers3587
Water10,196566
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15280 Å2
ΔGint-149 kcal/mol
Surface area34080 Å2
MethodPISA
2
D: Putative hexonate dehydrogenase
B: Putative hexonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9837
Polymers54,7522
Non-polymers2305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-58 kcal/mol
Surface area21110 Å2
MethodPISA
3
D: Putative hexonate dehydrogenase
A: Putative hexonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9425
Polymers54,7522
Non-polymers1903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-34 kcal/mol
Surface area21320 Å2
MethodPISA
4
A: Putative hexonate dehydrogenase
C: Putative hexonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8804
Polymers54,7522
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-40 kcal/mol
Surface area21210 Å2
MethodPISA
5
B: Putative hexonate dehydrogenase
C: Putative hexonate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9216
Polymers54,7522
Non-polymers1684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-53 kcal/mol
Surface area21330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.650, 94.197, 129.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11C-476-

HOH

Detailsbiological unit is an tetramer

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Components

#1: Protein
Putative hexonate dehydrogenase


Mass: 27376.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis (bacteria)
Strain: P125109 / Gene: SEN1435 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5R540, UniProt: A0A6C7HQ69*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein (10mM Tris pH 7.9 and 5mM MgCl2, Reservoir (0.1 M Bis-Tris Propane:HCl pH 7 1.098 M Malonic acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid,0.24 M ...Details: Protein (10mM Tris pH 7.9 and 5mM MgCl2, Reservoir (0.1 M Bis-Tris Propane:HCl pH 7 1.098 M Malonic acid, 0.15 M Ammonium Citrate Tribasic, 0.072 M Succinic Acid, 0.18 M DL-Malic Acid,0.24 M Sodium Acetate, 0.3 M Sodium Formate, 0.096 M Ammonium Tartrate Dibasic), Cryoprotection (Reservoir, + 20% Ethylene glycol), sitting drop, vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

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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: Jan 1, 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: 1.9→94.197 Å / Num. all: 71511 / Num. obs: 71511 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-26.50.6641.266989103070.66499.7
2-2.126.70.4311.86509697530.43199.8
2.12-2.276.90.2982.66306291830.29899.9
2.27-2.457.10.223.56105886160.22100
2.45-2.697.30.1684.65768379250.168100
2.69-37.40.1146.55298071940.114100
3-3.477.30.0788.74687663910.078100
3.47-4.257.30.06110.23960554490.06199.9
4.25-6.017.20.05211.63057842740.052100
6.01-129.3566.60.04512.51603824190.04597.6

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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: 3CXR

3cxr


Resolution: 1.9→64.678 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8665 / SU ML: 0.17 / σ(F): 0 / σ(I): 0 / Phase error: 20.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 3612 5.06 %RANDOM
Rwork0.1635 ---
all0.1654 71403 --
obs0.1654 71403 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.67 Å2 / Biso mean: 20.5572 Å2 / Biso min: 3.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→64.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 18 566 8224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077779
X-RAY DIFFRACTIONf_angle_d1.03310553
X-RAY DIFFRACTIONf_chiral_restr0.0721232
X-RAY DIFFRACTIONf_plane_restr0.0041348
X-RAY DIFFRACTIONf_dihedral_angle_d14.2472768
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9250.25541540.2232565271999
1.925-1.95140.23911350.20725642699100
1.9514-1.97930.23161500.206825552705100
1.9793-2.00880.25411240.225762700100
2.0088-2.04020.26241600.190925572717100
2.0402-2.07360.24021300.191625742704100
2.0736-2.10940.2271450.179125982743100
2.1094-2.14780.23581420.167925572699100
2.1478-2.18910.20811300.171925972727100
2.1891-2.23380.2021260.166126052731100
2.2338-2.28230.22011570.162725672724100
2.2823-2.33540.19741120.155926022714100
2.3354-2.39380.20131300.160526262756100
2.3938-2.45860.20071420.155125832725100
2.4586-2.53090.2091280.166925982726100
2.5309-2.61260.2341290.158726332762100
2.6126-2.7060.21531320.172426012733100
2.706-2.81430.22031360.170326172753100
2.8143-2.94240.19181690.166425872756100
2.9424-3.09750.20381350.163126222757100
3.0975-3.29160.18651340.162426172751100
3.2916-3.54570.17931480.153426362784100
3.5457-3.90250.18611360.145826582794100
3.9025-4.46710.17341400.13826652805100
4.4671-5.62760.17391370.144226952832100
5.6276-64.71550.19221510.17452736288797
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)
11.638-0.05470.24320.8527-0.63771.69280.0048-0.1150.25880.1271-0.09930.1055-0.1373-0.30660.03840.09740.02480.02690.1899-0.00710.1051-7.178112.914947.3527
22.78750.71650.87671.40120.33732.20290.0308-0.30080.68060.1642-0.13050.4499-0.4148-0.30190.08540.17340.00870.04040.2372-0.03850.26-9.118316.708356.3902
30.8609-0.60360.45220.5042-0.00551.4918-0.1072-0.39050.03770.19950.15050.0666-0.0666-0.35080.07420.11920.04750.00970.1829-0.02030.07214.412410.753655.5227
41.4439-0.02460.14441.519-0.13711.2332-0.0771-0.2022-0.03420.11410.08270.0227-0.0482-0.1172-0.00970.07240.01490.00220.1174-0.00650.072810.08868.615848.318
51.10910.0443-0.0711.4388-0.47780.9205-0.0007-0.14950.25710.2602-0.0147-0.0087-0.1749-0.150.01030.10660.0295-0.00970.0938-0.03330.12564.548321.345638.0704
61.84630.0418-0.10821.2518-0.15241.9236-0.14720.2139-0.0235-0.1843-0.0480.2244-0.0393-0.15330.12130.12010.0061-0.05250.1821-0.00450.1243-7.116511.848211.4833
71.04220.1947-0.17120.6862-0.56211.0315-0.09840.1207-0.0805-0.28060.07760.09320.1886-0.15360.02620.1161-0.0199-0.00850.0579-0.02780.06417.93757.636720.0247
81.68940.1468-0.24090.52920.34291.7178-0.0156-0.03480.12540.0403-0.1502-0.3090.04160.49890.11760.11140.0103-0.02390.27440.03250.230443.88028.537846.5805
93.12630.4728-1.5460.2139-0.01021.8849-0.0202-0.4737-0.5280.1234-0.0532-0.27460.40410.17980.00020.16930.0373-0.04550.35230.02560.33245.96513.413154.7903
100.32660.1455-0.57330.6220.00672.0695-0.0038-0.38760.4470.3495-0.0799-0.4058-0.38920.72630.01480.2837-0.0536-0.17510.3357-0.05940.347340.473917.664157.6992
113.50711.3071-0.05692.0774-0.14511.37140.0718-0.2675-0.44070.18370.0991-0.12190.2545-0.0379-0.09610.1428-0.0026-0.02160.13160.03440.114519.6361-0.059154.2699
121.17130.1137-0.25451.0101-0.45611.1441-0.0748-0.14260.13280.1140.0312-0.1943-0.10150.2152-0.02760.0726-0.0199-0.04320.0888-0.01410.126827.976314.496246.7185
131.49450.29220.04291.8840.33211.41960.0068-0.1062-0.18940.1514-0.1311-0.2450.29540.2951-0.10720.13820.02010.04180.06960.02630.099331.78811.57136.4761
141.7751-0.29220.00050.15480.31640.95150.0446-0.10090.294-0.0769-0.2219-0.19650.01490.4452-0.12050.10690.04970.14510.28830.12670.2643.620815.147516.8979
151.4905-0.67830.87160.6414-0.32352.006-0.01190.36240.7225-0.1283-0.1839-0.4358-0.31610.45010.07620.18860.01510.0950.27260.12490.441245.684420.14098.3387
161.78790.12880.59640.1813-0.15271.28770.08240.5766-0.076-0.4083-0.2138-0.26350.5030.3650.55590.32990.25480.2860.34790.07610.100839.93266.08765.9289
173.0669-1.24830.17511.498-0.31480.69740.02830.3550.4042-0.2401-0.004-0.2627-0.05450.0157-0.02310.1582-0.00670.01080.10960.03820.13419.06823.47329.5384
181.02120.11140.06930.59-0.19621.0043-0.05680.09820.0274-0.2159-0.0314-0.11580.17290.14490.0190.14110.02690.0590.07250.01110.0727.73289.100917.0964
191.1203-0.3704-0.02011.86280.48051.16250.03060.07610.3346-0.3669-0.1958-0.2722-0.27620.209-0.12220.1253-0.02390.01220.09660.04460.189431.805522.09527.4358
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 4 through 43 )D0
2X-RAY DIFFRACTION2chain 'D' and (resid 44 through 70 )D0
3X-RAY DIFFRACTION3chain 'D' and (resid 71 through 107 )D0
4X-RAY DIFFRACTION4chain 'D' and (resid 108 through 181 )D0
5X-RAY DIFFRACTION5chain 'D' and (resid 182 through 256 )D0
6X-RAY DIFFRACTION6chain 'A' and (resid 4 through 93 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 94 through 256 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 4 through 43 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 44 through 70 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 71 through 93 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 94 through 119 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 120 through 181 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 256 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 43 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 44 through 70 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 71 through 93 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 94 through 119 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 120 through 181 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 182 through 256 )C0

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