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- PDB-2re2: CRYSTAL STRUCTURE OF A PUTATIVE IRON-MOLYBDENUM COFACTOR (FEMO-CO... -

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Basic information

Entry
Database: PDB / ID: 2re2
TitleCRYSTAL STRUCTURE OF A PUTATIVE IRON-MOLYBDENUM COFACTOR (FEMO-CO) DINITROGENASE (TA1041M) FROM THERMOPLASMA ACIDOPHILUM DSM 1728 AT 1.30 A RESOLUTION
ComponentsUncharacterized protein Ta1041
KeywordsOXIDOREDUCTASE / DINITROGENASE IRON-MOLYBDENUM COFACTOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyMTH1175 domain / Dinitrogenase iron-molybdenum cofactor biosynthesis domain / Dinitrogenase iron-molybdenum cofactor biosynthesis / Dinitrogenase iron-molybdenum cofactor biosynthesis superfamily / Dinitrogenase iron-molybdenum cofactor / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta / Nitro_FeMo-Co domain-containing protein
Function and homology information
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function (NP_394501.1) from Thermoplasma acidophilum at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein Ta1041
B: Uncharacterized protein Ta1041


Theoretical massNumber of molelcules
Total (without water)30,1142
Polymers30,1142
Non-polymers00
Water6,053336
1
A: Uncharacterized protein Ta1041


Theoretical massNumber of molelcules
Total (without water)15,0571
Polymers15,0571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein Ta1041


Theoretical massNumber of molelcules
Total (without water)15,0571
Polymers15,0571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.381, 36.555, 51.641
Angle α, β, γ (deg.)72.030, 71.810, 87.250
Int Tables number1
Space group name H-MP1
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Uncharacterized protein Ta1041


Mass: 15057.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM 1728, IFO 15155, JCM 9062, AMRC-C165 / Gene: NP_394501.1, Ta1041 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9HJC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: NANODROP, 19.0% 2-Propanol, 19.0% PEG 4000, 5.0% Glycerol, 0.1M Citric acid pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 19, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.3→46.676 Å / Num. obs: 56000 / % possible obs: 94.8 % / Redundancy: 2 % / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.331.90.4031.9755739920.40391.8
1.33-1.371.90.3312.2759739200.33192.5
1.37-1.411.90.243.1754838790.2492.9
1.41-1.4520.2093.5729237240.20993.2
1.45-1.520.1714.3710336390.17193.5
1.5-1.551.90.1444.9692735550.14494
1.55-1.611.90.1195.6672034530.11994.5
1.61-1.6820.1035.9647333170.10394.4
1.68-1.7520.0867.4624831850.08695.3
1.75-1.8420.0629.8603830870.06295.5
1.84-1.9420.0549.9574729230.05496
1.94-2.0620.04412.7548227820.04496.1
2.06-2.220.04210.5514626060.04296.8
2.2-2.3720.0518.9479724330.05197.2
2.37-2.620.04211.9456823120.04297.6
2.6-2.9120.03514.2403020330.03597.8
2.91-3.3620.02521.8362518290.02598
3.36-4.1120.02420.9300115270.02498.1
4.11-5.8120.02518.2230311750.02597.4
5.81-46.6761.90.0262312166290.02694.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.3→46.676 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.533 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.05
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2809 5 %RANDOM
Rwork0.161 ---
obs0.162 56000 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.157 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.19 Å2-0.19 Å2
2---0.27 Å20.45 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 336 2094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221953
X-RAY DIFFRACTIONr_bond_other_d0.0010.021288
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.9782676
X-RAY DIFFRACTIONr_angle_other_deg0.99133206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57525.86775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64715329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.206154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022286
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
X-RAY DIFFRACTIONr_nbd_refined0.230.2380
X-RAY DIFFRACTIONr_nbd_other0.1880.21386
X-RAY DIFFRACTIONr_nbtor_refined0.180.2997
X-RAY DIFFRACTIONr_nbtor_other0.0910.21029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1450.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.222
X-RAY DIFFRACTIONr_mcbond_it1.3071.51309
X-RAY DIFFRACTIONr_mcbond_other0.3281.5519
X-RAY DIFFRACTIONr_mcangle_it1.73722079
X-RAY DIFFRACTIONr_scbond_it3.4173706
X-RAY DIFFRACTIONr_scangle_it4.5824.5592
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 196 -
Rwork0.251 3796 -
all-3992 -
obs--91.81 %
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)
11.4607-0.17680.41360.3546-0.33521.03760.00120.1434-0.0254-0.0306-0.01550.0180.05030.00160.0143-0.05840.00320.0031-0.022-0.0027-0.05385.249835.81261.6859
20.558-0.19660.06131.192-0.45371.0984-0.0008-0.0413-0.02060.0907-0.00580.0309-0.0149-0.02480.0066-0.0443-0.0062-0.0021-0.06290.0031-0.053912.526728.567425.4184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-3 - 11416 - 133
2X-RAY DIFFRACTION2BB-5 - 11414 - 133

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