PDB-4h3v: Crystal structure of oxidoreductase domain protein from Kribbella...

ID or keywords:

Entry

Database: PDB / ID: 4h3v

Title

Crystal structure of oxidoreductase domain protein from Kribbella flavida

Components

Oxidoreductase domain protein

Keywords

Structural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

oxidoreductase activity
Similarity search - Function

Biological species

Kribbella flavida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.68 Å

Authors

Michalska, K. / Mack, J.C. / McKnight, S.M. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of oxidoreductase domain protein from Kribbella flavida
Authors: Michalska, K. / Mack, J.C. / McKnight, S.M. / Endres, M. / Joachimiak, A.

History

Deposition	Sep 14, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 26, 2012	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4h3v.cif.gz	301.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4h3v.ent.gz	255.8 KB	Display	PDB format
PDBx/mmJSON format	4h3v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4h3v_validation.pdf.gz	433.6 KB	Display	wwPDB validaton report
Full document	4h3v_full_validation.pdf.gz	437.1 KB	Display
Data in XML	4h3v_validation.xml.gz	31.7 KB	Display
Data in CIF	4h3v_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h3/4h3v ftp://data.pdbj.org/pub/pdb/validation_reports/h3/4h3v	HTTPS FTP

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Related structure data

Similar structure data	4gqa-1 4gqa-2 6a3f-1 4cqn-1 5xn0-2 6ktj-d 6ktk-d 6a3g-d 5yap-d Search similar-shape structures by Omokage search (details) 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	TargetTrack: MCSG-APC103531

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Oxidoreductase domain protein

B: Oxidoreductase domain protein

hetero molecules

84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Oxidoreductase domain protein

B: Oxidoreductase domain protein

hetero molecules

A: Oxidoreductase domain protein

B: Oxidoreductase domain protein

hetero molecules

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

2

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	70.597, 70.597, 288.538
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-402- FMT
2	1	B-401- FMT
3	1	B-636- HOH

#1: Protein	Oxidoreductase domain protein Mass: 42156.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida (bacteria) / Strain: DSM 17836 / Gene: Kfla_4276 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) Magic / References: UniProt: D2PU28
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.13 Å³/Da / Density % sol: 42.31 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 0.1 M Mg formate, 19% PEG3350, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.68→30 Å / Num. all: 84563 / Num. obs: 84453 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / R_merge(I) obs: 0.09 / Net I/σ(I): 21.9
Reflection shell	Resolution: 1.68→1.71 Å / Redundancy: 5 % / R_merge(I) obs: 0.59 / Mean I/σ(I) obs: 2.59 / Num. unique all: 4093 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELX		model building
MLPHARE		phasing
DM		model building
BUCCANEER		model building
Coot		model building
PHENIX	(phenix.refine: dev_1096)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing
BUCCANEER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.68→29.235 Å / SU ML: 0.12 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.91 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1774	1677	1.99 %	random
R_work	0.1436	-	-	-
all	0.1443	84322	-	-
obs	0.1443	84322	99.88 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.68→29.235 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5787	0	9	518	6314

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	5984
X-RAY DIFFRACTION	f_angle_d	1.391	8138
X-RAY DIFFRACTION	f_dihedral_angle_d	13.044	2139
X-RAY DIFFRACTION	f_chiral_restr	0.085	899
X-RAY DIFFRACTION	f_plane_restr	0.008	1075

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6803-1.7297	0.2205	144	0.1852	6735	X-RAY DIFFRACTION	100
1.7297-1.7856	0.2118	141	0.1709	6760	X-RAY DIFFRACTION	100
1.7856-1.8494	0.2043	142	0.1531	6789	X-RAY DIFFRACTION	100
1.8494-1.9234	0.174	125	0.1446	6819	X-RAY DIFFRACTION	100
1.9234-2.0109	0.1898	121	0.1379	6808	X-RAY DIFFRACTION	100
2.0109-2.1169	0.1656	141	0.1282	6800	X-RAY DIFFRACTION	100
2.1169-2.2495	0.1606	156	0.1261	6851	X-RAY DIFFRACTION	100
2.2495-2.4231	0.1837	119	0.1294	6891	X-RAY DIFFRACTION	100
2.4231-2.6668	0.1717	123	0.1421	6897	X-RAY DIFFRACTION	100
2.6668-3.0523	0.1928	143	0.1496	6954	X-RAY DIFFRACTION	100
3.0523-3.8442	0.1663	170	0.1408	7009	X-RAY DIFFRACTION	100
3.8442-29.2394	0.1723	152	0.1497	7332	X-RAY DIFFRACTION	99

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	0.3235	0.4589	-0.208	0.9641	0.029	0.7444	-0.0153	0.0497	0.0309	-0.0864	0.0241	0.0028	-0.1136	0.0383	-0.0097	0.1402	-0.0041	0.0042	0.1767	0.005	0.1862	60.3001	50.0868	128.5348
2	1.8701	-1.1797	0.5473	2.7696	-0.5002	1.9017	-0.038	0.1622	0.1602	-0.1889	-0.0177	-0.0894	-0.2867	-0.0396	0.0624	0.1579	-0.0271	0.0226	0.1481	-0.0064	0.102	39.6826	39.6083	120.5092
3	0.615	0.1776	-0.126	0.2868	-0.0858	0.3508	0.0033	0.0002	-0.0739	-0.0189	-0.0222	-0.0809	0.0657	0.057	0.0254	0.1369	0.0107	0.005	0.1228	0.0007	0.1376	48.1513	33.7719	139.609
4	5.2251	3.1635	3.6482	2.4512	2.4025	4.5603	-0.1165	0.3153	-0.3377	-0.1564	0.2176	-0.2063	0.0554	0.0813	-0.0752	0.1542	-0.0371	0.053	0.1651	-0.0194	0.139	49.0096	31.7602	113.028
5	0.761	-1.0925	-1.249	6.2145	2.6553	3.8912	0.0096	-0.0841	0.0516	-0.0389	0.1316	-0.2721	0.0185	0.0835	-0.1609	0.1321	-0.0526	0.0016	0.1579	0.011	0.1303	7.287	6.9032	134.2237
6	1.3124	-0.8441	-0.4228	5.0933	2.3544	3.2568	0.0315	0.0386	-0.1594	0.1135	-0.0627	-0.0364	0.3447	-0.0345	0.037	0.1475	-0.0633	0.023	0.167	0.0193	0.1648	6.6167	-0.8636	133.8443
7	3.5028	1.301	-1.6232	2.0432	-1.2461	2.619	-0.1109	-0.0308	-0.1754	-0.1649	0.0516	-0.1417	0.2401	0.0704	0.0502	0.1918	-0.0323	0.0061	0.1862	-0.0296	0.1617	8.5835	3.4083	120.6958
8	0.7497	0.2274	0.194	0.3901	0.141	0.548	-0.0551	0.0743	-0.0326	-0.0575	0.0427	0.0168	0.0486	-0.0399	0.0092	0.1624	-0.0268	0.014	0.1751	-0.0009	0.1361	19.0632	20.4274	124.4138
9	2.8769	-2.2685	0.4264	6.4546	-0.0246	1.6378	0.0154	0.2271	-0.3472	-0.2606	0.0071	0.0242	0.3097	-0.0086	-0.0114	0.1722	-0.0571	0.0272	0.1761	-0.0388	0.1455	24.6658	14.3757	122.632
10	3.793	-2.4994	0.9187	4.5032	-1.5001	3.0274	0.0061	0.0811	-0.4556	-0.2047	0.0165	0.0322	0.4605	0.14	-0.0439	0.2043	-0.0499	0.0366	0.1655	-0.0791	0.1807	34.2988	13.052	120.038
11	0.6188	0.2826	0.0054	0.5494	0.0115	0.8318	-0.0443	0.0496	-0.013	-0.0367	0.0304	0.0358	0.0496	-0.0578	0.0092	0.1064	-0.0109	-0.0026	0.1134	-0.0061	0.1155	24.0912	27.6466	132.8364
12	2.962	0.8558	1.2712	0.3802	0.7193	2.3615	0.0057	0.0376	0.0943	-0.0753	-0.0034	0.0348	-0.0669	-0.0994	0.0101	0.1486	-0.0235	0.0074	0.1491	-0.0077	0.1368	6.44	17.2719	129.6307
13	7.2984	2.6897	-4.3972	1.7171	-1.3289	3.3884	-0.1774	0.4439	-0.0125	-0.1271	0.2084	-0.0501	0.0527	-0.1171	-0.0231	0.1771	-0.0586	0.0089	0.1697	-0.0501	0.0955	25.7354	19.5888	111.0932

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 149 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 150 through 265 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 266 through 359 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 360 through 387 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 28 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 29 through 63 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 64 through 108 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 109 through 176 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 177 through 204 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 205 through 238 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 239 through 334 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 335 through 359 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 360 through 387 )

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