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- PDB-4qey: Crystal structure of a DUF4425 family protein (BACOVA_05332) from... -

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Basic information

Entry
Database: PDB / ID: 4qey
TitleCrystal structure of a DUF4425 family protein (BACOVA_05332) from Bacteroides ovatus ATCC 8483 at 2.52 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF14466 family / DUF4425 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipoxygenase-1 - #60 / PLAT/LH2 and C2-like Ca2+-binding lipoprotein / PLAT/LH2 and C2-like Ca2+-binding lipoprotein / Lipoxygenase-1 / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_05332) from Bacteroides ovatus ATCC 8483 at 2.52 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,28945
Polymers142,76410
Non-polymers2,52535
Water3,495194
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7558
Polymers14,2761
Non-polymers4797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5074
Polymers14,2761
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4013
Polymers14,2761
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4453
Polymers14,2761
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7558
Polymers14,2761
Non-polymers4797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3382
Polymers14,2761
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4634
Polymers14,2761
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5514
Polymers14,2761
Non-polymers2743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3832
Polymers14,2761
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6937
Polymers14,2761
Non-polymers4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.590, 101.340, 91.420
Angle α, β, γ (deg.)90.000, 107.910, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 14276.384 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_05332 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M5D7
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (25-155) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (25-155) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.20M magnesium acetate, 22.0% polyethylene glycol 3350, 3.0% D(+)-sucrose, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.52→47.347 Å / Num. obs: 52432 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 66.022 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.67
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.52-2.610.7442226135126196.8
2.61-2.710.5832.5221395003198.6
2.71-2.840.3933.6228145456197.1
2.84-2.990.2655.3240555265199.8
2.99-3.170.1827.4231895084199.2
3.17-3.420.09513.1242785380199
3.42-3.760.06317.8219125123197.1
3.76-4.30.05122.2244005298199.6
4.3-5.40.03927.6229425251198.2
5.4-47.3470.04524.4234235429198

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.52→47.347 Å / Cor.coef. Fo:Fc: 0.9471 / Cor.coef. Fo:Fc free: 0.9279 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.POLYETHYLENE GLYCOL FRAGMENTS (PEG AND PGE) WERE MODELED INTO THE STRUCTURE; AND 1,2-ETHANEDIOL, USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 2670 5.1 %RANDOM
Rwork0.1962 ---
obs0.1975 52402 98.48 %-
Displacement parametersBiso max: 144.54 Å2 / Biso mean: 56.3311 Å2 / Biso min: 14.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.2236 Å20 Å20.5895 Å2
2---0.9795 Å20 Å2
3---0.7559 Å2
Refine analyzeLuzzati coordinate error obs: 0.389 Å
Refinement stepCycle: LAST / Resolution: 2.52→47.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9164 0 164 194 9522
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4572SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes296HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1397HARMONIC5
X-RAY DIFFRACTIONt_it9660HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1372SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10347SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9660HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg13022HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.29
X-RAY DIFFRACTIONt_other_torsion1.87
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2463 166 4.39 %
Rwork0.215 3612 -
all0.2164 3778 -
obs--98.48 %
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)
14.7836-0.94090.01362.641-0.14662.14980.0517-0.5081-0.3990.1068-0.11950.05630.06750.18120.0677-0.028-0.0412-0.0519-0.11260.1464-0.11489.25547.620768.1517
27.54871.01081.39923.9462-0.24122.14460.1630.1527-0.465-0.2340.0374-0.64720.17790.1172-0.2004-0.15570.13160.0115-0.20670.00110.004332.065348.856955.2206
33.82831.31491.76235.37222.24273.9246-0.04850.1511-0.1388-0.0380.156-0.48910.11340.347-0.1075-0.1918-0.0788-0.008-0.09930.0334-0.048437.462273.770952.1383
43.59220.4606-1.50742.75991.85626.90070.0293-0.07210.30080.1226-0.21990.1155-0.50260.18280.1905-0.0549-0.0516-0.0334-0.1744-0.0729-0.090218.329187.414563.0961
52.7614-0.05060.75844.0897-1.89874.31370.1981-0.54910.02760.2586-0.07690.2094-0.0787-0.0709-0.1211-0.09460.00950.1059-0.0275-0.0116-0.17710.994271.544973.0041
66.1746-1.09671.32794.10090.44243.62670.1784-0.253-0.27980.20250.01190.47660.0354-0.0543-0.1903-0.0883-0.15070.0462-0.22810.0232-0.0714-15.710250.177432.6373
75.9040.9780.74052.65720.30012.60950.07610.5518-0.4167-0.1158-0.0538-0.18980.10290.0624-0.0223-0.02210.058-0.0323-0.1376-0.106-0.14346.632647.135419.3506
82.8594-0.08430.70124.88092.21234.98590.23950.52870.1683-0.3448-0.1131-0.3309-0.18740.1339-0.1264-0.1249-0.00550.1483-0.0250.0644-0.208516.260870.262813.7629
93.0114-0.7665-1.84692.6475-0.86866.15010.05550.1490.2466-0.2133-0.1266-0.0525-0.4167-0.07230.0711-0.06720.03420.0009-0.16080.1082-0.08380.366487.678923.3814
102.8149-1.03071.91173.9894-1.51234.2334-0.0447-0.1053-0.15190.17170.10940.1788-0.0026-0.1918-0.0647-0.0930.0802-0.0128-0.1448-0.0129-0.0606-19.507675.353434.8139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|31-155}
2X-RAY DIFFRACTION2{B|32-155}
3X-RAY DIFFRACTION3{C|32-155}
4X-RAY DIFFRACTION4{D|33-155}
5X-RAY DIFFRACTION5{E|32-155}
6X-RAY DIFFRACTION6{F|32-155}
7X-RAY DIFFRACTION7{G|31-155}
8X-RAY DIFFRACTION8{H|31-155}
9X-RAY DIFFRACTION9{I|31-155}
10X-RAY DIFFRACTION10{J|32-155}

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