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

ID or keywords:

Entry

Database: PDB / ID: 3uuw

Title

1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.

Components

Putative oxidoreductase with NAD(P)-binding Rossmann-fold domain

Keywords

OXIDOREDUCTASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Clostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.63 Å

Authors

Minasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.
Authors: Minasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Nov 28, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 18, 2012	Group: Other
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Jan 24, 2018	Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4	Sep 13, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3uuw.cif.gz	555.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3uuw.ent.gz	458.1 KB	Display	PDB format
PDBx/mmJSON format	3uuw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uu/3uuw ftp://data.pdbj.org/pub/pdb/validation_reports/uu/3uuw	HTTPS FTP

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Related structure data

Related structure data	1tltS S: Starting model for refinement
Similar structure data	4l9r-1 3nt5-1 4mjl-d 3nt4-1 4l8v-d 3nt2-1 4miy-d 2hk9-d 3ntq-1 3mz0-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: idp05340

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Links

PDB pages	PDBj / wwPDB / NCBI

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

141 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

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 number	1
Space group name H-M	P1

Details

Chains A, B, C and D represent Biological Assembly

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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

#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 / Chloride 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 / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#6: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1191 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.75 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97855 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2011 / Details: Mirrors
Radiation	Monochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97855 Å / Relative weight: 1
Reflection	Resolution: 1.63→30 Å / Num. all: 155282 / Num. obs: 155282 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 22.3 Å² / R_merge(I) obs: 0.065 / Net I/σ(I): 16.7
Reflection shell	Resolution: 1.63→1.66 Å / Redundancy: 4.2 % / R_merge(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

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TLT

1tlt

Resolution: 1.63→29.97 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19457	7763	5 %	RANDOM
R_work	0.15804	-	-	-
all	0.15985	146631	-	-
obs	0.15985	146631	97.06 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 18.689 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.5 Å²	1.27 Å²	-0.36 Å²
2-	-	1.08 Å²	-0.2 Å²
3-	-	-	-0.75 Å²

Refinement step

Cycle: LAST / Resolution: 1.63→29.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9654	0	91	1191	10936

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	10449
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7232
X-RAY DIFFRACTION	r_angle_refined_deg	1.351	1.973	14112
X-RAY DIFFRACTION	r_angle_other_deg	0.835	3	17886
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.33	5	1334
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.443	25.629	453
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.467	15	2088
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.647	15	41
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	1614
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	11578
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1931
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.995	1.5	6406
X-RAY DIFFRACTION	r_mcbond_other	0.316	1.5	2601
X-RAY DIFFRACTION	r_mcangle_it	1.794	2	10486
X-RAY DIFFRACTION	r_scbond_it	2.954	3	4043
X-RAY DIFFRACTION	r_scangle_it	4.775	4.5	3625
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.63→1.672 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	539	-
R_work	0.23	10620	-
obs	-	-	95.35 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.6722	-0.0961	0.5341	0.6287	0.1672	2.3238	0.0039	0.0284	0.0161	-0.0321	-0.0143	-0.1271	0.0479	0.2434	0.0104	0.0138	-0.0051	0.0279	0.0458	-0.0158	0.0654	31.792	-19.6359	-17.772
2	0.8091	-0.3881	0.1689	0.9315	-0.0412	1.1391	0.0118	0.0594	0.0499	-0.0942	-0.018	-0.074	0.0578	0.1649	0.0062	0.0154	0.0013	0.0105	0.0558	-0.0151	0.0169	10.9032	-7.9777	-19.0045
3	1.6919	0.238	0.4962	1.8699	0.7803	2.7496	-0.0115	0.2354	0.0363	-0.1717	0.0584	-0.0815	-0.0036	0.0452	-0.0469	0.0234	-0.0134	0.0142	0.0552	0.0012	0.0204	7.9345	-0.6292	-25.9995
4	0.8373	-0.4325	-0.0433	0.5996	0.0529	0.241	-0.0177	-0.0399	-0.0179	-0.0348	0.036	-0.0091	0.0134	-0.0244	-0.0183	0.0304	-0.0055	0.0059	0.0139	-0.0049	0.0091	9.4436	-13.5388	-14.8228
5	1.1124	-0.1481	-0.4467	0.5339	0.0581	1.6382	0.0154	0.0208	0.0152	-0.0124	-0.0511	0.1238	-0.026	-0.2152	0.0357	0.0219	0.0006	-0.0292	0.082	0.0052	0.0722	-33.0474	19.0659	-15.212
6	0.3761	-0.214	-0.013	0.6352	-0.0377	0.4704	-0.0137	0.0204	0.0278	-0.0733	0.0196	0.0571	-0.0525	-0.0924	-0.0059	0.0393	-0.0095	-0.0128	0.0446	0.0213	0.0328	-14.0459	11.7127	-20.0864
7	2.0784	0.1418	0.1617	1.9431	-0.2856	1.8318	-0.0587	0.2681	-0.0156	-0.24	0.0877	0.0868	0.004	0.0047	-0.029	0.0405	-0.0255	-0.0101	0.0465	0.0012	0.0042	-8.8268	1.1828	-25.5331
8	0.8713	-0.3092	0.1106	0.6101	-0.0438	0.6076	-0.0206	-0.0393	0.0515	-0.0464	0.0263	0.0016	-0.0273	-0.0313	-0.0058	0.0216	-0.0108	-0.0069	0.0192	0.0119	0.0197	-10.0013	14.4874	-14.1203
9	1.7153	-0.4835	0.4415	1.1765	0.2856	2.312	-0.0387	0.0023	-0.2273	0.0249	0.0281	-0.1145	0.219	0.2169	0.0105	0.0816	0.032	0.0024	0.0243	0.0131	0.1089	33.3025	-22.5674	9.7215
10	1.4513	-0.8307	-0.1787	1.2562	-0.2194	0.8684	-0.0304	-0.1295	-0.0228	0.074	-0.0158	-0.1105	0.0942	0.1923	0.0463	0.0725	0.0053	-0.0371	0.0669	0.0026	0.0613	25.1851	-10.0345	22.5327
11	1.2395	-0.2176	0.1631	0.7883	-0.273	1.1789	0.0314	-0.0798	-0.0349	0.101	-0.0411	0.0192	0.0431	0.0227	0.0097	0.0546	-0.0076	-0.0066	0.0096	-0.0001	0.013	6.9941	-5.3062	19.1285
12	0.8468	-0.031	0.1783	0.7195	-0.1355	1.4688	0.0577	-0.0509	-0.0334	0.0247	-0.0337	-0.1123	0.0278	0.0913	-0.024	0.0359	0.0113	-0.0187	0.022	0.0037	0.0296	23.9105	-7.2171	18.1614
13	0.83	-0.0068	0.0229	0.7876	-0.5387	2.2906	0.0192	-0.0416	0.1221	0.0766	-0.03	0.0694	-0.1888	-0.1257	0.0108	0.0426	0.0066	0.0268	0.0142	-0.0129	0.0459	-31.4608	20.3166	18.0562
14	1.9942	-0.5039	0.2071	0.8345	-0.0382	1.1623	0.0095	-0.1716	0.187	0.0439	-0.0041	-0.0424	-0.1616	-0.1559	-0.0053	0.059	0.0192	0.0194	0.0348	-0.0119	0.0247	-12.2014	6.2071	18.8288
15	2.7855	0.2136	-0.3415	1.5519	-0.2737	2.8828	0.0361	-0.3309	0.2229	0.2541	-0.0062	0.0052	-0.0699	-0.0176	-0.0298	0.0945	0.0087	0.0066	0.0496	-0.0379	0.0396	-4.1639	6.9256	25.927
16	1.3227	-0.5199	-0.19	0.4357	0.0041	0.1595	0.0497	-0.044	-0.0025	-0.0133	-0.0352	0.0363	0.0337	-0.0092	-0.0145	0.0305	-0.0113	0.0029	0.0235	-0.0056	0.0066	-17.0386	2.765	14.8438

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 120
2	X-RAY DIFFRACTION	2	A	121 - 175
3	X-RAY DIFFRACTION	3	A	176 - 220
4	X-RAY DIFFRACTION	4	A	221 - 305
5	X-RAY DIFFRACTION	5	B	2 - 107
6	X-RAY DIFFRACTION	6	B	108 - 175
7	X-RAY DIFFRACTION	7	B	176 - 220
8	X-RAY DIFFRACTION	8	B	221 - 304
9	X-RAY DIFFRACTION	9	C	2 - 69
10	X-RAY DIFFRACTION	10	C	70 - 143
11	X-RAY DIFFRACTION	11	C	144 - 253
12	X-RAY DIFFRACTION	12	C	254 - 304
13	X-RAY DIFFRACTION	13	D	2 - 120
14	X-RAY DIFFRACTION	14	D	121 - 175
15	X-RAY DIFFRACTION	15	D	176 - 220
16	X-RAY DIFFRACTION	16	D	221 - 304

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