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- PDB-3c2q: Crystal structure of conserved putative LOR/SDH protein from Meth... -

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Basic information

Entry
Database: PDB / ID: 3c2q
TitleCrystal structure of conserved putative LOR/SDH protein from Methanococcus maripaludis S2
ComponentsUncharacterized conserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative LOR/SDH / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


conserved putative lor/sdh protein from methanococcus maripaludis s2 domain / putative lor/sdh protein like domains / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / : / : / LOR/SDH bifunctional enzyme conserved region / Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold / Arginine dihydrolase ArgZ-like, C-terminal, first region / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold ...conserved putative lor/sdh protein from methanococcus maripaludis s2 domain / putative lor/sdh protein like domains / Conserved hypothetical protein CHP00300 / LOR/SDH bifunctional enzyme, conserved domain / : / : / LOR/SDH bifunctional enzyme conserved region / Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold / Arginine dihydrolase ArgZ-like, C-terminal, first region / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / NICKEL (II) ION / Uncharacterized protein
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsDuke, N. / Gu, M. / Mulligan, R. / Conrad, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of conserved putative LOR/SDH protein from Methanococcus maripaludis S2
Authors: Duke, N. / Gu, M. / Mulligan, R. / Conrad, B. / Joachimiak, A.
History
DepositionJan 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 conserved protein
B: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6477
Polymers76,3122
Non-polymers3355
Water5,765320
1
A: Uncharacterized conserved protein
B: Uncharacterized conserved protein
hetero molecules

A: Uncharacterized conserved protein
B: Uncharacterized conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,29414
Polymers152,6244
Non-polymers67010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.592, 119.592, 161.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Components

#1: Protein Uncharacterized conserved protein


Mass: 38156.066 Da / Num. of mol.: 2 / Fragment: Residues 74-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Species: Methanococcus maripaludis / Strain: S2 / LL / Gene: MMP1218, gi:45047647 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q6LXX7
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.00M Sodium citrate, 0.10M Imidazole pH 8.0, 0.05M Sodium fluoride, cryoprotected with 25% v/v Glycerol and saturated Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979229 Å
DetectorType: SBC-3 / Detector: CCD / Date: Aug 21, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979229 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 80188 / Num. obs: 75521 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 2→2.1 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 6.2 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2→96.23 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.566 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21694 3994 5 %RANDOM
Rwork0.19086 ---
obs0.19215 74815 99.78 %-
all-75521 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2→96.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5045 0 21 320 5386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225145
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9836957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.195661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30225.401187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90515953
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9061519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023711
X-RAY DIFFRACTIONr_nbd_refined0.2050.22360
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.238
X-RAY DIFFRACTIONr_mcbond_it1.3281.53399
X-RAY DIFFRACTIONr_mcangle_it1.73225356
X-RAY DIFFRACTIONr_scbond_it3.50331944
X-RAY DIFFRACTIONr_scangle_it5.0144.51601
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 300 -
Rwork0.241 5426 -
obs--98.61 %

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