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- PDB-3u4y: The crystal structure of a functionally unknown protein (Dtox_175... -

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Basic information

Entry
Database: PDB / ID: 3u4y
TitleThe crystal structure of a functionally unknown protein (Dtox_1751) from Desulfotomaculum acetoxidans DSM 771.
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / protein structure initiative / midwest center for structural genomi cs / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / : / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesDesulfotomaculum acetoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.994 Å
AuthorsTan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein (Dtox_1751) from Desulfotomaculum acetoxidans DSM 771.
Authors: Tan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A.
History
DepositionOct 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4444
Polymers72,2002
Non-polymers2442
Water1448
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3443
Polymers36,1001
Non-polymers2442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)36,1001
Polymers36,1001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)139.636, 66.661, 80.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsExperimentally unknown. It is predicted to be a monomer.

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Components

#1: Protein uncharacterized protein


Mass: 36099.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfotomaculum acetoxidans (bacteria)
Strain: DSM 771 / Gene: Dtox_1751 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C8VX32
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Succinic acid 15% (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915, 0.97929
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2011 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
ReflectionResolution: 2.994→48.5 Å / Num. all: 15627 / Num. obs: 15627 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 12.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / Num. unique all: 754 / % possible all: 97.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.994→48.214 Å / SU ML: 0.95 / σ(F): 1.34 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 775 4.97 %random
Rwork0.1758 ---
all0.1804 15583 --
obs0.1804 15583 98.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.811 Å2 / ksol: 0.303 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.6985 Å2-0 Å20 Å2
2---8.6619 Å2-0 Å2
3---17.3604 Å2
Refinement stepCycle: LAST / Resolution: 2.994→48.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 16 8 4862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094946
X-RAY DIFFRACTIONf_angle_d1.3096735
X-RAY DIFFRACTIONf_dihedral_angle_d18.0391757
X-RAY DIFFRACTIONf_chiral_restr0.082807
X-RAY DIFFRACTIONf_plane_restr0.006880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9935-3.18110.39761140.28022310X-RAY DIFFRACTION94
3.1811-3.42660.30921310.22372430X-RAY DIFFRACTION100
3.4266-3.77130.31761350.19662453X-RAY DIFFRACTION100
3.7713-4.31670.24811340.15662461X-RAY DIFFRACTION100
4.3167-5.43750.19361290.12312518X-RAY DIFFRACTION100
5.4375-48.22010.2571320.17062636X-RAY DIFFRACTION100
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)
12.1693-0.4755-0.44771.3326-0.57040.72030.0482-0.21420.2030.04750.13590.5972-0.0869-0.12440.1691-0.0410.03350.25830.1548-0.09310.5889.029239.896289.0083
22.3785-0.8522-0.97163.14320.96612.25470.1069-0.03210.2479-0.0173-0.07740.46270.0873-0.15090.12530.25640.00840.00390.0628-0.20280.70376.401637.631780.5706
30.6512-0.33020.39430.7318-0.37710.29950.01130.2828-0.4389-0.231-0.1110.72050.0795-0.01980.06490.2277-0.0224-0.02440.2235-0.11570.44414.189235.283773.6675
40.33570.1165-0.00560.88330.2080.4236-0.02610.2613-0.0131-0.286-0.06230.4457-0.0082-0.33130.0188-0.0819-0.3358-0.4492-0.6377-0.7022-0.172924.879138.207770.3365
51.6105-0.42640.66763.08360.43510.56750.02970.09430.1077-0.1562-0.11340.1642-0.1060.11690.22090.1680.05130.0730.1892-0.0046-0.034934.62144.730680.2043
61.11870.09560.08451.55240.10811.56020.05860.10510.0021-0.1796-0.1093-0.021-0.2020.0890.00610.1315-0.07350.05690.160.02750.159234.076346.608380.3917
70.93180.6549-0.25761.40620.31330.57310.0686-0.1586-0.00090.2133-0.1570.10390.0655-0.0108-0.0625-0.1685-0.3530.2546-0.1940.02380.117631.356343.089590.7316
81.0477-0.4129-0.15955.4784-0.47461.20690.0108-0.06570.07460.13060.14920.08130.00490.02880.26810.2194-0.14280.2020.0689-0.09180.486820.167643.471994.4052
91.27380.2718-0.05241.65690.24140.68610.1538-0.20830.24760.3246-0.06420.4171-0.0144-0.06910.43650.1671-0.12490.38460.2062-0.14570.445317.603143.893995.9739
102.03931.05320.34532.2441-0.76682.17190.6021-0.69220.37070.9557-0.27420.5321-0.2398-0.1245-0.16230.712-0.30090.27310.7024-0.03680.40318.129217.0601126.056
112.7968-1.6036-0.12172.2065-0.09191.95470.272-0.9550.22230.69660.06240.2816-0.29950.1870.14480.7929-0.43030.41440.7539-0.3050.568314.376826.1264123.5308
122.37460.6741-0.54020.9446-0.13151.36950.5396-1.11280.52910.5312-0.26130.0535-0.36380.44340.09310.3454-0.3422-0.07810.2687-0.3093-0.279624.986621.7495110.8347
131.21751.1704-0.65271.56580.04671.60490.0809-0.6782-0.47870.3744-0.2592-0.4680.30320.44860.38710.2194-0.09180.0270.49520.37010.23226.8896.9556108.5936
144.4892-0.80381.07681.5683-0.70554.0561-0.0379-0.2017-0.2626-0.1691-0.5046-0.60420.92530.8738-0.73540.4857-0.12230.01450.53670.34610.317522.5612-0.0243112.6028
150.2728-0.0829-0.12510.0625-0.11070.72250.2417-0.3167-0.2968-0.4842-0.1797-0.53850.5454-0.1633-0.02610.4696-0.17990.03650.30790.12510.501413.54734.7778110.5803
160.7696-0.2287-0.55292.5095-0.68092.0524-0.0036-0.4907-0.24460.48470.02140.15390.1762-0.1809-0.06230.5085-0.35480.0010.65090.29810.06229.88755.2185122.1414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:49)
2X-RAY DIFFRACTION2chain 'A' and (resseq 50:71)
3X-RAY DIFFRACTION3chain 'A' and (resseq 72:105)
4X-RAY DIFFRACTION4chain 'A' and (resseq 106:180)
5X-RAY DIFFRACTION5chain 'A' and (resseq 181:201)
6X-RAY DIFFRACTION6chain 'A' and (resseq 202:230)
7X-RAY DIFFRACTION7chain 'A' and (resseq 231:274)
8X-RAY DIFFRACTION8chain 'A' and (resseq 275:293)
9X-RAY DIFFRACTION9chain 'A' and (resseq 294:322)
10X-RAY DIFFRACTION10chain 'B' and (resseq 6:53)
11X-RAY DIFFRACTION11chain 'B' and (resseq 54:93)
12X-RAY DIFFRACTION12chain 'B' and (resseq 94:191)
13X-RAY DIFFRACTION13chain 'B' and (resseq 192:230)
14X-RAY DIFFRACTION14chain 'B' and (resseq 231:250)
15X-RAY DIFFRACTION15chain 'B' and (resseq 251:274)
16X-RAY DIFFRACTION16chain 'B' and (resseq 275:322)

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