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- PDB-3msq: Crystal structure of a Putative ubiquinone biosynthesis protein (... -

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Entry
Database: PDB / ID: 3msq
TitleCrystal structure of a Putative ubiquinone biosynthesis protein (Npun02000094) from Nostoc punctiforme PCC 73102 at 2.85 A resolution
ComponentsPutative ubiquinone biosynthesis protein
KeywordsBIOSYNTHETIC PROTEIN / Coq4 superfamily / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyUbiquinone biosynthesis protein Coq4 / Coenzyme Q (ubiquinone) biosynthesis protein Coq4 / ubiquinone biosynthetic process / membrane / Ubiquinone biosynthesis protein
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative ubiquinone biosynthesis protein (Npun02000094) from Nostoc punctiforme PCC 73102 at 2.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 16, 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: Putative ubiquinone biosynthesis protein
B: Putative ubiquinone biosynthesis protein
C: Putative ubiquinone biosynthesis protein
D: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)103,1614
Polymers103,1614
Non-polymers00
Water00
1
A: Putative ubiquinone biosynthesis protein
D: Putative ubiquinone biosynthesis protein

A: Putative ubiquinone biosynthesis protein
D: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)103,1614
Polymers103,1614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area7910 Å2
ΔGint-73 kcal/mol
Surface area34340 Å2
MethodPISA
2
A: Putative ubiquinone biosynthesis protein

A: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,5812
Polymers51,5812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2620 Å2
ΔGint-33 kcal/mol
Surface area18470 Å2
MethodPISA
3
B: Putative ubiquinone biosynthesis protein
C: Putative ubiquinone biosynthesis protein

B: Putative ubiquinone biosynthesis protein
C: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)103,1614
Polymers103,1614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area7890 Å2
ΔGint-73 kcal/mol
Surface area34660 Å2
MethodPISA
4
B: Putative ubiquinone biosynthesis protein

B: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,5812
Polymers51,5812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area2630 Å2
ΔGint-33 kcal/mol
Surface area18660 Å2
MethodPISA
5
C: Putative ubiquinone biosynthesis protein

C: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,5812
Polymers51,5812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area2620 Å2
ΔGint-33 kcal/mol
Surface area18640 Å2
MethodPISA
6
D: Putative ubiquinone biosynthesis protein

D: Putative ubiquinone biosynthesis protein


Theoretical massNumber of molelcules
Total (without water)51,5812
Polymers51,5812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area2650 Å2
ΔGint-33 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.720, 82.030, 187.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein
Putative ubiquinone biosynthesis protein


Mass: 25790.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: ATCC 29133 / PCC 73102 / Gene: 23130561, Npun_R0350 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B2J5W7
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT 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: 3.05 Å3/Da / Density % sol: 59.65 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20.0000% polyethylene glycol 3000, 0.1M citric acid pH 5.5, Additive: 0.001 M Ubiquinone, 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: 0.91837,0.97937,0.97882
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979371
30.978821
ReflectionResolution: 2.85→49.266 Å / Num. obs: 26383 / % possible obs: 82.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 86.669 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.85-2.921.110.998232356783.8
2.92-30.8391.287846340783.8
3-3.090.6881.617652331183.4
3.09-3.190.4632.317499325083.5
3.19-3.290.3323.157403316383.4
3.29-3.410.2614.127076303282.7
3.41-3.540.1895.386667287883.1
3.54-3.680.1327.516571279382.9
3.68-3.840.1059.366221265282.4
3.84-4.030.08511.16022256082.2
4.03-4.250.06913.45714241581.8
4.25-4.510.05515.35337225881.6
4.51-4.820.04817.35080213981.3
4.82-5.20.04916.84706197581.7
5.2-5.70.05217.44327182381.3
5.7-6.370.04817.33948165181.2
6.37-7.360.04120.23468145181.3
7.36-9.010.03524.82916120780.3
9.01-12.750.02730.9223393180.4
12.75-49.270.02831115248875.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.85→49.266 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0.75 / 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. B-FACTORS CONTAIN BOTH TLS AND RESIDUAL COMPONENTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1323 5.02 %RANDOM
Rwork0.195 ---
obs0.197 26370 --
Displacement parametersBiso max: 192.91 Å2 / Biso mean: 74.634 Å2 / Biso min: 35.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.586 Å20 Å20 Å2
2---4.733 Å20 Å2
3---4.147 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 0 0 6552
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2266SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes164HARMONIC2
X-RAY DIFFRACTIONt_gen_planes958HARMONIC5
X-RAY DIFFRACTIONt_it6704HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion856SEMIHARMONIC5
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_contact7601SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6704HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9090HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion20.03
LS refinement shellResolution: 2.85→2.97 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.265 157 5.24 %
Rwork0.246 2841 -
all0.247 2998 -
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)
11.02010.4072-1.13821.19460.18311.78750.0371-0.12320.2180.0640.0799-0.070.09590.1457-0.117-0.01630.0165-0.0183-0.0039-0.0295-0.1067-27.4763-39.923837.5483
23.0349-0.02910.00460.42690.4421.9852-0.0075-0.29790.4743-0.1720.1401-0.2751-0.19250.141-0.1327-0.1910.01910.0071-0.0195-0.128-0.01934.5221-30.535712.4399
32.7328-0.1727-0.2791.47570.23911.20510.094-0.22930.50720.0722-0.13760.2232-0.2182-0.00150.0436-0.0681-0.03940.0104-0.0748-0.0742-0.0783-35.9678-25.05474.1026
42.14640.3276-0.09954.31740.0541.2828-0.1599-0.0295-0.14110.05040.20541.0885-0.083-0.2052-0.04550.02230.02170.0597-0.31160.1-0.0206-57.1673-80.720747.0603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A6 - 221
2X-RAY DIFFRACTION2{ B|* }B6 - 221
3X-RAY DIFFRACTION3{ C|* }C6 - 221
4X-RAY DIFFRACTION4{ D|* }D6 - 221

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