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- PDB-4r5o: Crystal structure of a Quinonprotein alcohol dehydrogenase-like p... -

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Entry
Database: PDB / ID: 4r5o
TitleCrystal structure of a Quinonprotein alcohol dehydrogenase-like protein (BT1487) from Bacteroides thetaiotaomicron VPI-5482 at 2.64 A resolution
ComponentsQuinonprotein alcohol dehydrogenase-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / Immunoglobulin-like beta-sandwich fold / PF16407 family / DUF5015 / 7-bladed beta-propeller / YVTN repeat family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyBacteroidetes PKD-like domain / PKD-like domain / Domain of unknown function (DUF5074) / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / Chem-7PE / ACETATE ION / Quinonprotein alcohol dehydrogenase-like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Quinonprotein alcohol dehydrogenase-like protein (BT1487) from Bacteroides thetaiotaomicron VPI-5482 at 2.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Quinonprotein alcohol dehydrogenase-like protein
B: Quinonprotein alcohol dehydrogenase-like protein
C: Quinonprotein alcohol dehydrogenase-like protein
D: Quinonprotein alcohol dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,21427
Polymers189,9824
Non-polymers4,23223
Water6,197344
1
A: Quinonprotein alcohol dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,74111
Polymers47,4961
Non-polymers1,24510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Quinonprotein alcohol dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2069
Polymers47,4961
Non-polymers1,7108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Quinonprotein alcohol dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4625
Polymers47,4961
Non-polymers9674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Quinonprotein alcohol dehydrogenase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8062
Polymers47,4961
Non-polymers3101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.545, 155.545, 94.635
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Quinonprotein alcohol dehydrogenase-like protein


Mass: 47495.566 Da / Num. of mol.: 4 / Fragment: residues 23-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1487 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A7N7

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Non-polymers , 5 types, 367 molecules

#2: Chemical
ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H30O7
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (23-448) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (23-448) 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: 3.48 Å3/Da / Density % sol: 64.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.20 M calcium acetate, 40.00% polyethylene glycol 300, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97941,0.97868
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978681
ReflectionResolution: 2.64→29.395 Å / Num. obs: 73803 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 69.403 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 11.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.64-2.740.4051.82545313665196.5
2.74-2.850.3012.42698014586196
2.85-2.980.2173.42612814333195.3
2.98-3.140.1534.92467214202192.6
3.14-3.340.1047.42724914640196.6
3.34-3.590.06711.22571613976195.8
3.59-3.950.04915.32566714113193.8
3.95-4.520.03520.72499013944192.7
4.52-5.670.029242566013947193.5
5.67-29.3950.02425.92560314311193.5

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Phasing

PhasingMethod: MAD

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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: MAD / Resolution: 2.64→29.395 Å / Cor.coef. Fo:Fc: 0.9365 / Cor.coef. Fo:Fc free: 0.921 / 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 MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. CALCIUM (CA), ACETATE (ACT), AND POLYETHYLENE GLYCROL (7PE) FROM THE CRYSTALLIZATION HAVE BEEN MODELED INTO THE STRUCTURE. 6. CHLORIDE (CL) FROM THE EXPRESSION/PURIFICATION HAS BEEN MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 3712 5.03 %RANDOM
Rwork0.1764 ---
obs0.1777 73763 98.17 %-
Displacement parametersBiso max: 154.81 Å2 / Biso mean: 58.5263 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1--1.5648 Å20 Å20 Å2
2---1.5648 Å20 Å2
3---3.1297 Å2
Refine analyzeLuzzati coordinate error obs: 0.341 Å
Refinement stepCycle: LAST / Resolution: 2.64→29.395 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12968 0 138 344 13450
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6127SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes381HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1925HARMONIC5
X-RAY DIFFRACTIONt_it13384HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC10
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1798SEMIHARMONIC5
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_contact14968SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13384HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18151HARMONIC21.23
X-RAY DIFFRACTIONt_omega_torsion3.67
X-RAY DIFFRACTIONt_other_torsion1.89
LS refinement shellResolution: 2.64→2.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2564 257 4.97 %
Rwork0.2114 4912 -
all0.2136 5169 -
obs--98.17 %
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)
10.25010.0246-0.06820.8001-0.25591.0412-0.03780.060.00030.3063-0.0580.1111-0.13920.12340.0958-0.0159-0.01420.055-0.1445-0.0207-0.036540.841523.245831.2878
20.3268-0.36110.35812.2195-1.17321.39720.02590.0547-0.03740.0890.00840.02060.0431-0.1286-0.0343-0.1262-0.0169-0.0042-0.10890.0368-0.01350.4045127.710944.8725
30.26720.3133-0.20161.9545-0.42990.5113-0.0755-0.0114-0.0083-0.31250.01450.03910.1911-0.070.0610.0602-0.1001-0.0879-0.17520.0203-0.044142.922266.022557.152
42.2298-1.0909-0.83211.10431.06411.3826-0.01530.1994-0.15740.053-0.11730.1134-0.0847-0.09860.1326-0.2450.0397-0.06410.0602-0.0134-0.150718.7562113.914113.1982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|23 - 448}A23 - 448
2X-RAY DIFFRACTION2{B|33 - 448}B33 - 448
3X-RAY DIFFRACTION3{C|33 - 448}C33 - 448
4X-RAY DIFFRACTION4{D|24 - 448}D24 - 448

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