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- PDB-2avn: CRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYL... -

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Basic information

Entry
Database: PDB / ID: 2avn
TitleCRYSTAL STRUCTURE OF A UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN (TM1389) FROM THERMOTOGA MARITIMA MSB8 AT 2.35 A RESOLUTION
Componentsubiquinone/menaquinone biosynthesis methyltransferase-related protein
KeywordsTRANSFERASE / UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHYLTRANSFERASE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methyltransferase activity / methylation
Similarity search - Function
Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOSELENOCYSTEINE / Ubiquinone/menaquinone biosynthesis methyltransferase-related protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Ubiquinone/menaquinone biosynthesis methyltransferase-related protein (tm1389) from THERMOTOGA MARITIMA at 2.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 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
Revision 1.4Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
B: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1395
Polymers61,1822
Non-polymers9583
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-16 kcal/mol
Surface area21970 Å2
MethodPISA
2
A: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
B: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
hetero molecules

A: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
B: ubiquinone/menaquinone biosynthesis methyltransferase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,27910
Polymers122,3644
Non-polymers1,9156
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area7690 Å2
ΔGint-56 kcal/mol
Surface area41270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.475, 130.475, 192.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-249-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISARGARGAA0 - 24612 - 258
21HISHISARGARGBB0 - 24612 - 258
12SAISAISAISAIAD1300
22SAISAISAISAIBE2300

NCS ensembles :
ID
1
2

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Components

#1: Protein ubiquinone/menaquinone biosynthesis methyltransferase-related protein


Mass: 30590.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1389 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1A9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-SAI / S-ADENOSYL-L-HOMOSELENOCYSTEINE


Mass: 431.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5Se
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.9668.67
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop, nanodrop51.0M LiCl, 10.0% PEG-600, 0.1M Citrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.0
2932vapor diffusion, sitting drop, nanodrop740.0% MPD, 0.1M HEPES, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 7.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97915
SYNCHROTRONSSRL BL11-120.979318, 0.918370
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJul 4, 2005
ADSC QUANTUM 3152CCDJun 14, 2005flat mirror
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.9793181
30.918371
ReflectionResolution: 2.35→29.8 Å / Num. obs: 40826 / % possible obs: 99.6 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.183 / Rsym value: 0.183 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.35-2.4195.35.60.9810.726010.981
2.41-2.4899.85.70.8660.829140.866
2.48-2.5599.85.70.7460.928280.746
2.55-2.6399.95.70.5751.227370.575
2.63-2.7199.95.70.4551.626880.455
2.71-2.8199.95.70.3951.825880.395
2.81-2.9110012.80.8850.725180.885
2.91-3.0310012.90.663124090.663
3.03-3.1710012.90.4991.323250.499
3.17-3.3210012.90.329222210.329
3.32-3.510012.80.234321360.234
3.5-3.7210012.80.1853.820260.185
3.72-3.9710012.70.1444.819070.144
3.97-4.2910012.60.112617810.112
4.29-4.710012.50.0966.816580.096
4.7-5.2510012.40.0946.915080.094
5.25-6.0710012.30.0996.913480.099
6.07-7.4310011.90.1055.511600.105
7.43-10.5110011.40.087.89290.08
10.51-29.8695.810.10.0668.75440.066

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.35→29.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.057 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. AN S-ADENOSYLHOMOCYSTEINE COFACTOR WAS MODELED INTO DENSITY ON BOTH SUBUNITS IN THE ASYMMETRIC UNIT. AN ANOMALOUS DIFFERENCE DENSITY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. AN S-ADENOSYLHOMOCYSTEINE COFACTOR WAS MODELED INTO DENSITY ON BOTH SUBUNITS IN THE ASYMMETRIC UNIT. AN ANOMALOUS DIFFERENCE DENSITY PEAK WAS OBSERVED AT THE POSITION OF THE SULFUR ATOM OF THE CO-FACTOR. THEREFORE, THE COFACTOR WAS MODELED AS SE-ADENOSYLHOMOCYSTEINE. 3. A PHOSPHATE ANION FROM THE PURIFICATION BUFFER WAS MODELED NEAR SEVERAL ARGININE SIDECHAINS AT A SPECIAL POSITION BETWEEN SYMMETRY-RELATED SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2048 5 %RANDOM
Rwork0.169 ---
all0.171 ---
obs-38735 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.977 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.96 Å20 Å2
2--1.91 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3991 0 57 210 4258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224162
X-RAY DIFFRACTIONr_bond_other_d0.0010.023787
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9725636
X-RAY DIFFRACTIONr_angle_other_deg0.838761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1323.469196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0951530
X-RAY DIFFRACTIONr_chiral_restr0.0870.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
X-RAY DIFFRACTIONr_nbd_refined0.2040.2771
X-RAY DIFFRACTIONr_nbd_other0.1780.23687
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21987
X-RAY DIFFRACTIONr_nbtor_other0.0850.22435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.28
X-RAY DIFFRACTIONr_mcbond_it2.16532540
X-RAY DIFFRACTIONr_mcbond_other0.52931010
X-RAY DIFFRACTIONr_mcangle_it2.97253996
X-RAY DIFFRACTIONr_scbond_it5.3281877
X-RAY DIFFRACTIONr_scangle_it7.3111636
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
13771MEDIUM POSITIONAL0.460.5
13771MEDIUM THERMAL0.852
240MEDIUM POSITIONAL0.080.5
240MEDIUM THERMAL1.072
LS refinement shellResolution: 2.35→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 149 -
Rwork0.243 2731 -
obs--97.69 %
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)
10.6732-0.78711.01622.7119-2.17934.43660.0761-0.0299-0.0748-0.0026-0.167-0.1122-0.21710.23590.0909-0.07360.0574-0.0606-0.1440.0765-0.088838.96226.4693.357
21.4124-0.43950.77530.8791-0.43263.04210.08-0.0140.0101-0.04430.0660.03560.0551-0.0034-0.146-0.12960.0512-0.0654-0.23210.0053-0.114523.87140.367-29.814
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 24612 - 258
21AD13001
32BB0 - 24612 - 258
42BE23001

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