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- PDB-3uuw: 1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM... -

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Basic information

Entry
Database: PDB / ID: 3uuw
Title1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.
ComponentsPutative oxidoreductase with NAD(P)-binding Rossmann-fold domain
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / YceM-like, C-terminal domain / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...: / YceM-like, C-terminal domain / : / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Oxidoreductase with NAD(P)-binding Rossmann-fold domain
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMinasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2023
Title: A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.
Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / ...Authors: Rosas-Lemus, M. / Dey, S. / Minasov, G. / Tan, K. / Anderson, S.M. / Brunzelle, J. / Nocadello, S. / Shabalin, I. / Filippova, E. / Halavaty, A. / Kim, Y. / Maltseva, N. / Osipiuk, J. / Minor, W. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionNov 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 1, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain
B: Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain
C: Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain
D: Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,40827
Polymers139,7664
Non-polymers1,64223
Water21,4561191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-131 kcal/mol
Surface area46860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.521, 69.535, 83.098
Angle α, β, γ (deg.)98.10, 106.97, 115.73
Int Tables number1
Space group name H-MP1
DetailsChains A, B, C and D represent Biological Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain


Mass: 34941.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_34500, mviM / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q180U8

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Non-polymers , 6 types, 1214 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 0.3M Sodium chloride, 0.01M HEPES (pH 7.5), Screen solution: 0.2M Calcium chloride, 2% Glycerol, 20% PEG 3350, 0.01M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97855 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2011 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97855 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. all: 155282 / Num. obs: 155282 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.75 / Num. unique all: 7631 / % possible all: 94.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TLT

1tlt


Resolution: 1.63→29.97 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.886 / SU ML: 0.045
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19457 7763 5 %RANDOM
Rwork0.15804 ---
all0.15985 146631 --
obs0.15985 146631 97.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å21.27 Å2-0.36 Å2
2--1.08 Å2-0.2 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.63→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9654 0 91 1191 10936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210449
X-RAY DIFFRACTIONr_bond_other_d0.0010.027232
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.97314112
X-RAY DIFFRACTIONr_angle_other_deg0.835317886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3351334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44325.629453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.467152088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6471541
X-RAY DIFFRACTIONr_chiral_restr0.0860.21614
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211578
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021931
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9951.56406
X-RAY DIFFRACTIONr_mcbond_other0.3161.52601
X-RAY DIFFRACTIONr_mcangle_it1.794210486
X-RAY DIFFRACTIONr_scbond_it2.95434043
X-RAY DIFFRACTIONr_scangle_it4.7754.53625
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 539 -
Rwork0.23 10620 -
obs--95.35 %
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)
10.6722-0.09610.53410.62870.16722.32380.00390.02840.0161-0.0321-0.0143-0.12710.04790.24340.01040.0138-0.00510.02790.0458-0.01580.065431.792-19.6359-17.772
20.8091-0.38810.16890.9315-0.04121.13910.01180.05940.0499-0.0942-0.018-0.0740.05780.16490.00620.01540.00130.01050.0558-0.01510.016910.9032-7.9777-19.0045
31.69190.2380.49621.86990.78032.7496-0.01150.23540.0363-0.17170.0584-0.0815-0.00360.0452-0.04690.0234-0.01340.01420.05520.00120.02047.9345-0.6292-25.9995
40.8373-0.4325-0.04330.59960.05290.241-0.0177-0.0399-0.0179-0.03480.036-0.00910.0134-0.0244-0.01830.0304-0.00550.00590.0139-0.00490.00919.4436-13.5388-14.8228
51.1124-0.1481-0.44670.53390.05811.63820.01540.02080.0152-0.0124-0.05110.1238-0.026-0.21520.03570.02190.0006-0.02920.0820.00520.0722-33.047419.0659-15.212
60.3761-0.214-0.0130.6352-0.03770.4704-0.01370.02040.0278-0.07330.01960.0571-0.0525-0.0924-0.00590.0393-0.0095-0.01280.04460.02130.0328-14.045911.7127-20.0864
72.07840.14180.16171.9431-0.28561.8318-0.05870.2681-0.0156-0.240.08770.08680.0040.0047-0.0290.0405-0.0255-0.01010.04650.00120.0042-8.82681.1828-25.5331
80.8713-0.30920.11060.6101-0.04380.6076-0.0206-0.03930.0515-0.04640.02630.0016-0.0273-0.0313-0.00580.0216-0.0108-0.00690.01920.01190.0197-10.001314.4874-14.1203
91.7153-0.48350.44151.17650.28562.312-0.03870.0023-0.22730.02490.0281-0.11450.2190.21690.01050.08160.0320.00240.02430.01310.108933.3025-22.56749.7215
101.4513-0.8307-0.17871.2562-0.21940.8684-0.0304-0.1295-0.02280.074-0.0158-0.11050.09420.19230.04630.07250.0053-0.03710.06690.00260.061325.1851-10.034522.5327
111.2395-0.21760.16310.7883-0.2731.17890.0314-0.0798-0.03490.101-0.04110.01920.04310.02270.00970.0546-0.0076-0.00660.0096-0.00010.0136.9941-5.306219.1285
120.8468-0.0310.17830.7195-0.13551.46880.0577-0.0509-0.03340.0247-0.0337-0.11230.02780.0913-0.0240.03590.0113-0.01870.0220.00370.029623.9105-7.217118.1614
130.83-0.00680.02290.7876-0.53872.29060.0192-0.04160.12210.0766-0.030.0694-0.1888-0.12570.01080.04260.00660.02680.0142-0.01290.0459-31.460820.316618.0562
141.9942-0.50390.20710.8345-0.03821.16230.0095-0.17160.1870.0439-0.0041-0.0424-0.1616-0.1559-0.00530.0590.01920.01940.0348-0.01190.0247-12.20146.207118.8288
152.78550.2136-0.34151.5519-0.27372.88280.0361-0.33090.22290.2541-0.00620.0052-0.0699-0.0176-0.02980.09450.00870.00660.0496-0.03790.0396-4.16396.925625.927
161.3227-0.5199-0.190.43570.00410.15950.0497-0.044-0.0025-0.0133-0.03520.03630.0337-0.0092-0.01450.0305-0.01130.00290.0235-0.00560.0066-17.03862.76514.8438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 120
2X-RAY DIFFRACTION2A121 - 175
3X-RAY DIFFRACTION3A176 - 220
4X-RAY DIFFRACTION4A221 - 305
5X-RAY DIFFRACTION5B2 - 107
6X-RAY DIFFRACTION6B108 - 175
7X-RAY DIFFRACTION7B176 - 220
8X-RAY DIFFRACTION8B221 - 304
9X-RAY DIFFRACTION9C2 - 69
10X-RAY DIFFRACTION10C70 - 143
11X-RAY DIFFRACTION11C144 - 253
12X-RAY DIFFRACTION12C254 - 304
13X-RAY DIFFRACTION13D2 - 120
14X-RAY DIFFRACTION14D121 - 175
15X-RAY DIFFRACTION15D176 - 220
16X-RAY DIFFRACTION16D221 - 304

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