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- PDB-4fxt: Crystal structure of a DUF3823 family protein (BACOVA_02663) from... -

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Basic information

Entry
Database: PDB / ID: 4fxt
TitleCrystal structure of a DUF3823 family protein (BACOVA_02663) from Bacteroides ovatus ATCC 8483 at 2.77 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12866 FAMILY / DUF3823 / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


Immunoglobulin-like - #2060 / DUF3823, N-terminal / Domain of unknown function DUF3823_C / Protein of unknown function (DUF3823) N-terminal domain / Domain of unknown function (DUF3823_C) / Carboxypeptidase-like, regulatory domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.77 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_02663) from Bacteroides ovatus ATCC 8483 at 2.77 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 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
K: Uncharacterized protein
L: Uncharacterized protein
M: Uncharacterized protein
N: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,13730
Polymers311,14414
Non-polymers99316
Water4,161231
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4114
Polymers22,2251
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2872
Polymers22,2251
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.810, 351.002, 90.343
Angle α, β, γ (deg.)90.000, 93.420, 90.000
Int Tables number4
Space group name H-MP1211
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Uncharacterized protein


Mass: 22224.555 Da / Num. of mol.: 14 / Fragment: UNP residues 24-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: BACOVA_02663 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LXU7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 24-224) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-224) 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.200M sodium formate, 20.00% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9792,0.91162,0.97901
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.911621
30.979011
ReflectionResolution: 2.77→49.079 Å / Num. obs: 82740 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 72.896 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.77-2.870.0111.7318488246199.7
2.87-2.980.0112.3307807983199.9
2.98-3.120.0113.3330718562199.9
3.12-3.280.0114.6310838049199.8
3.28-3.490.0116.7327808484199.9
3.49-3.750.0119.8310728026199.9
3.75-4.130.01112.9322638351199.9
4.13-4.720.01118.43179382321100
4.72-5.920.01121320758298199.9
5.92-49.0790.01127.8322688509199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.77→49.079 Å / Cor.coef. Fo:Fc: 0.9148 / Cor.coef. Fo:Fc free: 0.9008 / Occupancy max: 1 / Occupancy min: 0.5 / 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. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. 1,2-ETHANEDIOL, USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 4158 5.03 %RANDOM
Rwork0.1828 ---
obs0.1845 82633 99.81 %-
Displacement parametersBiso max: 198.23 Å2 / Biso mean: 74.245 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1--14.1189 Å20 Å211.0088 Å2
2--23.1448 Å20 Å2
3----9.0259 Å2
Refine analyzeLuzzati coordinate error obs: 0.451 Å
Refinement stepCycle: LAST / Resolution: 2.77→49.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20831 0 64 231 21126
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d9781SINUSOIDAL12
X-RAY DIFFRACTIONt_trig_c_planes590HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3060HARMONIC5
X-RAY DIFFRACTIONt_it21253HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2835SEMIHARMONIC5
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_contact23146SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d21253HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg28770HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion1.89
LS refinement shellResolution: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 317 5.28 %
Rwork0.2521 5684 -
all0.255 6001 -
obs--99.81 %
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)
13.37280.12820.88724.0078-0.88471.41990.1107-0.4353-0.4158-0.0021-0.0857-0.16880.08080.1636-0.025-0.2757-0.0280.14460.02640.02190.01645.28531.94267.7858
21.6933-0.84960.7824.0268-1.05451.8353-0.15520.00620.0145-0.2409-0.01760.1216-0.1652-0.12410.1728-0.0048-0.0702-0.1408-0.18150.01260.042343.221971.031534.6225
31.5991-0.7135-0.39825.0380.40581.9509-0.0417-0.29890.31530.23350.08670.4261-0.0891-0.3159-0.0451-0.15490.0161-0.0997-0.1507-0.03110.078838.895896.551850.2413
41.3420.48320.34616.50680.61091.536-0.1334-0.20810.00380.74560.1397-0.3163-0.24340.0812-0.0063-0.00870.051-0.2539-0.196-0.0642-0.04954.0529122.59656.0786
51.51510.4093-0.17733.265-0.90381.7077-0.0420.1490.0405-0.26090.036-0.28490.03630.05720.00590.04190.00870.0057-0.20860.05060.030561.343347.112935.3152
61.35660.2060.31643.42931.20231.75160.2478-0.17620.14350.5411-0.04420.0026-0.0994-0.1576-0.20360.0364-0.03210.0021-0.17520.05260.014548.4098-2.684262.4932
71.68312.1164-0.5824.7024-0.74251.16270.05470.1952-0.00250.03050.0216-0.562-0.02170.1531-0.0764-0.19650.049-0.1229-0.1929-0.08160.239864.3575147.80941.5557
81.80941.4063-0.22144.9654-1.59012.96430.3135-0.2482-0.281-0.2074-0.04230.00970.70890.0253-0.2712-0.1642-0.06260.0924-0.08460.0281-0.007730.52115.683415.5928
91.86230.7890.5064.4602-0.13691.9162-0.0385-0.00440.18560.12160.0523-0.2267-0.33810.3644-0.0138-0.0693-0.0391-0.0251-0.26180.01520.125764.631820.832253.9107
102.5647-1.49230.18132.5960.41671.4236-0.0590.16480.0709-0.528-0.09570.02830.02940.01750.1547-0.0021-0.05010.0631-0.1854-0.0010.046935.223556.003579.8507
111.17560.15270.52965.57691.42422.2019-0.24660.05640.1354-0.59240.1369-0.0997-0.1001-0.25920.10970.12470.0418-0.2961-0.2837-0.0348-0.043268.277979.714279.6658
120.97370.7670.33565.143-0.9671.1710.01860.083-0.21610.6450.1175-0.0257-0.2761-0.2555-0.13610.15850.1729-0.2962-0.2971-0.0562-0.00767.0793104.8736.4832
131.8808-0.16241.20017.0467-2.48723.14680.31810.063-0.39171.1076-0.1453-0.2872-0.01520.0379-0.17280.47170.1674-0.2707-0.3364-0.0513-0.118827.3754130.93613.4525
142.9277-0.10910.32086.8006-1.96912.6950.01190.1102-0.25270.7699-0.1174-0.9860.12350.28010.10550.03340.1904-0.2345-0.3172-0.0508-0.137634.7898158.06-0.9537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 224
2X-RAY DIFFRACTION2B28 - 224
3X-RAY DIFFRACTION3C28 - 224
4X-RAY DIFFRACTION4D28 - 224
5X-RAY DIFFRACTION5E0 - 224
6X-RAY DIFFRACTION6F24 - 224
7X-RAY DIFFRACTION7G29 - 224
8X-RAY DIFFRACTION8H29 - 224
9X-RAY DIFFRACTION9I29 - 224
10X-RAY DIFFRACTION10J28 - 224
11X-RAY DIFFRACTION11K27 - 224
12X-RAY DIFFRACTION12L29 - 224
13X-RAY DIFFRACTION13M25 - 224
14X-RAY DIFFRACTION14N29 - 224

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