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- PDB-5vm2: Crystal structure of ECK1772, an oxidoreductase/dehydrogenase of ... -

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Basic information

Entry
Database: PDB / ID: 5vm2
TitleCrystal structure of ECK1772, an oxidoreductase/dehydrogenase of unknown specificity involved in membrane biogenesis from Escherichia coli
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / NAD(H) or NADP(H)-dependent oxidoreductase / dehydrogenase / Rossman fold / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


L-iditol 2-dehydrogenase (NAD+) activity / Oxidoreductases / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / zinc ion binding
Similarity search - Function
Sorbitol dehydrogenase-like / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...Sorbitol dehydrogenase-like / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NAD(P)-dependent alcohol dehydrogenase / Uncharacterized zinc-type alcohol dehydrogenase-like protein YdjJ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.983 Å
AuthorsStogios, P.J. / Skarina, T. / McChesney, C. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSCN27220120026C United States
CitationJournal: To Be Published
Title: Crystal structure of ECK1772, an oxidoreductase/dehydrogenase of unknown specificity involved in membrane biogenesis from Escherichia coli
Authors: Stogios, P.J.
History
DepositionApr 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7087
Polymers75,4942
Non-polymers2155
Water11,746652
1
A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8363
Polymers37,7471
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8724
Polymers37,7471
Non-polymers1253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Alcohol dehydrogenase
hetero molecules

A: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6736
Polymers75,4942
Non-polymers1794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area3240 Å2
ΔGint-29 kcal/mol
Surface area28530 Å2
MethodPISA
4
B: Alcohol dehydrogenase
hetero molecules

B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7448
Polymers75,4942
Non-polymers2506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area3380 Å2
ΔGint-33 kcal/mol
Surface area28340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.994, 70.888, 149.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-403-

CL

21B-711-

HOH

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Components

#1: Protein Alcohol dehydrogenase / Putative oxidoreductase


Mass: 37746.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ARC77_00615, AU473_19815, BFL24_13020, ECs2483 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: C3T6X7, UniProt: P77280*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M sodium chloride, 0.1 M sodium citrate pH 5.6, 1 mM magnesium chloride, 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.98→40 Å / Num. obs: 47841 / % possible obs: 99.7 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Net I/σ(I): 22.7
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 2 / Num. unique obs: 2349 / CC1/2: 0.747 / Rpim(I) all: 0.293 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIXdev_2733refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3J

1e3j


Resolution: 1.983→39.312 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 1950 4.18 %RANDOM
Rwork0.1814 ---
obs0.1832 46646 97.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.983→39.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 5 652 5927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055418
X-RAY DIFFRACTIONf_angle_d0.9277340
X-RAY DIFFRACTIONf_dihedral_angle_d21.9132056
X-RAY DIFFRACTIONf_chiral_restr0.063843
X-RAY DIFFRACTIONf_plane_restr0.006956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9829-2.03250.26721230.24552877X-RAY DIFFRACTION89
2.0325-2.08750.33091270.2343014X-RAY DIFFRACTION93
2.0875-2.14890.26441330.22463063X-RAY DIFFRACTION94
2.1489-2.21820.2691390.21033124X-RAY DIFFRACTION96
2.2182-2.29750.2681400.20643143X-RAY DIFFRACTION97
2.2975-2.38950.24071380.20493166X-RAY DIFFRACTION98
2.3895-2.49820.27261390.20823182X-RAY DIFFRACTION98
2.4982-2.62990.25911410.21043216X-RAY DIFFRACTION99
2.6299-2.79460.27561420.20773252X-RAY DIFFRACTION99
2.7946-3.01040.2541440.20463262X-RAY DIFFRACTION100
3.0104-3.31320.21251410.18273277X-RAY DIFFRACTION99
3.3132-3.79220.20111450.16083314X-RAY DIFFRACTION100
3.7922-4.77650.17631470.14233341X-RAY DIFFRACTION100
4.7765-39.31930.21411510.17133465X-RAY DIFFRACTION99
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)
16.8986-0.5022-0.81813.34721.11311.60350.0645-0.04350.53840.72480.1956-0.4312-0.36620.3862-0.26880.63950.0001-0.07040.46110.01050.35861.531-2.267535.0954
20.4935-0.37010.01792.54030.97552.9069-0.1215-0.14760.06850.42080.12360.1346-0.0407-0.0706-0.00770.23340.02770.00960.31170.00650.302-8.909-5.385622.1246
37.6732-2.2299-3.00573.97350.1443.63030.08230.1356-0.4105-0.1869-0.2181-0.26510.3510.26170.15390.28990.0258-0.04150.2279-0.02820.38152.2808-22.76114.4283
48.1601-1.025-0.9877.151-1.77275.9935-0.0248-0.3020.1571-0.0141-0.0176-0.6927-0.37121.1607-0.10510.1738-0.0144-0.0020.36540.01890.36273.1605-8.95341.7506
50.61050.4235-0.90691.8849-1.57764.71430.0622-0.0487-0.05790.09870.0184-0.00210.11940.2255-0.0590.25620.0325-0.02760.28-0.02090.3233-4.1546-10.594713.5065
67.1082.86675.69248.04621.46266.73490.03020.0828-0.14891.13510.5118-1.17860.72951.0652-0.43340.47890.1079-0.17760.4375-0.08090.47038.2279-16.175730.5421
76.47650.2409-0.94663.70380.52264.1498-0.10110.46240.3969-0.9264-0.09290.1401-0.2256-0.30420.11760.59910.0665-0.0670.22860.00620.2929-31.9893-26.3905-22.8345
88.17224.8043-0.00837.65040.72466.5628-0.2880.22090.2835-1.01120.10550.3954-0.195-0.10350.19270.37760.0519-0.01670.23760.02350.2367-27.1087-11.0992-19.6038
90.6477-0.1292-0.71422.42231.21013.0099-0.04660.0496-0.0096-0.12620.0345-0.22870.09910.16310.00520.27360.01770.0210.23210.03220.2822-25.1234-21.6463-5.0877
107.452-0.9756-1.98645.91571.75194.11580.0911-0.2909-0.1050.4511-0.1310.07840.00760.03720.06980.2607-0.01850.02260.15620.03370.1576-36.9642-18.946613.4679
117.72330.1594-1.53546.8548-0.75235.21860.19260.1912-0.1658-0.1999-0.16440.8497-0.0267-0.6742-0.01540.1901-0.003-0.02050.219-0.00860.3035-36.5986-4.73675.1537
123.38221.58920.82295.39330.50633.01090.1194-0.0076-0.2695-0.1376-0.17720.19020.2598-0.3110.02770.22780.02680.03110.2232-0.03360.2114-33.3399-28.4102-7.7552
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:76)
2X-RAY DIFFRACTION2(chain A and resid 77:189)
3X-RAY DIFFRACTION3(chain A and resid 190:235)
4X-RAY DIFFRACTION4(chain A and resid 236:274)
5X-RAY DIFFRACTION5(chain A and resid 275:321)
6X-RAY DIFFRACTION6(chain A and resid 322:347)
7X-RAY DIFFRACTION7(chain B and resid 1:88)
8X-RAY DIFFRACTION8(chain B and resid 89:122)
9X-RAY DIFFRACTION9(chain B and resid 123:194)
10X-RAY DIFFRACTION10(chain B and resid 195:236)
11X-RAY DIFFRACTION11(chain B and resid 237:288)
12X-RAY DIFFRACTION12(chain B and resid 289:347)

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