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- PDB-3cet: Crystal structure of the pantheonate kinase-like protein Q6M145 a... -

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Basic information

Entry
Database: PDB / ID: 3cet
TitleCrystal structure of the pantheonate kinase-like protein Q6M145 at the resolution 1.8 A. Northeast Structural Genomics Consortium target MrR63
ComponentsConserved archaeal protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q6M145 / MrR63 / NESG / XRAY / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


conserved archaeal protein q6m145 / 4-[[4-(2-aminoethyl)phenoxy]-methyl]-2-furanmethanamine-glutamate synthase / Hydantoinase A/oxoprolinase / Hydantoinase/oxoprolinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Conserved archaeal protein
Similarity search - Component
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, J.F. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the pantheonate kinase-like protein Q6M145 at the resolution 1.8 A. Northeast Structural Genomics Consortium target MrR63.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Forouhar, F. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, J.F. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Conserved archaeal protein
B: Conserved archaeal protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6024
Polymers74,4102
Non-polymers1922
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-16 kcal/mol
Surface area27070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.424, 75.308, 163.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conserved archaeal protein


Mass: 37204.984 Da / Num. of mol.: 2
Mutation: K48N, I50V, D93N, G101S, Y106N, D146E, L182S, N187D, T254N, K268E, K269N, I284L, G294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Species: Methanococcus maripaludis / Strain: S2 / LL / Gene: MMP0072 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6M145
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% PEG 6000, 100 mM MnSO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 78605 / % possible obs: 89.5 % / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100409.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing and also in refinement (122276 reflections were used in refinement). BULK SOLVENT MODEL WAS USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 6115 5 %RANDOM
Rwork0.219 ---
obs0.219 68826 82.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.653 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-2.82 Å20 Å20 Å2
2---0.65 Å20 Å2
3----2.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4866 0 10 304 5180
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 827 4.9 %
Rwork0.243 16203 -
obs--68.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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