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- PDB-2oyn: Crystal structure of CDP-bound protein MJ0056 from Methanococcus ... -

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Basic information

Entry
Database: PDB / ID: 2oyn
TitleCrystal structure of CDP-bound protein MJ0056 from Methanococcus jannaschii, Pfam DUF120
ComponentsHypothetical protein MJ0056Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


CTP-dependent riboflavin kinase / riboflavin kinase activity / FMN biosynthetic process / riboflavin biosynthetic process / phosphorylation / nucleotide binding / magnesium ion binding
Similarity search - Function
Riboflavin kinase, archaeal / Riboflavin kinase domain, CTP-dependent / Riboflavin kinase, CTP-dependent / Domain of unknown function DUF120 / Riboflavin kinase-like / Riboflavin kinase domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / Riboflavin kinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of hypothetical protein from Methanococcus jannaschii bound to CDP
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT, SHOWN IN REMARK 350, IS PUTATIVE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein MJ0056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3513
Polymers16,9251
Non-polymers4262
Water1,910106
1
A: Hypothetical protein MJ0056
hetero molecules

A: Hypothetical protein MJ0056
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7026
Polymers33,8502
Non-polymers8524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)63.480, 63.480, 73.117
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-341-

HOH

Detailsprobable monomer

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Components

#1: Protein Hypothetical protein MJ0056 / Hypothesis


Mass: 16924.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: MJ0056 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q60365
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 100mM Hepes pH 7.5, 10% Isopropanol, 17% PEG 4000, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 16, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.85→47.946 Å / Num. all: 13339 / Num. obs: 13339 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.137 / Rsym value: 0.137 / Net I/σ(I): 26.6
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 28.1 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 4.6 / Num. unique all: 1907 / Rsym value: 0.866 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.867 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 656 4.9 %RANDOM
Rwork0.197 ---
obs0.199 13294 99.98 %-
all-13294 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 26 106 1245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221184
X-RAY DIFFRACTIONr_angle_refined_deg1.6462.0311598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84325.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.95154
X-RAY DIFFRACTIONr_chiral_restr0.1150.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02849
X-RAY DIFFRACTIONr_nbd_refined0.2090.2464
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2101
X-RAY DIFFRACTIONr_metal_ion_refined0.0830.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.218
X-RAY DIFFRACTIONr_mcbond_it0.9221.5690
X-RAY DIFFRACTIONr_mcangle_it1.71721128
X-RAY DIFFRACTIONr_scbond_it2.6863501
X-RAY DIFFRACTIONr_scangle_it4.2954.5466
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 48 -
Rwork0.214 911 -
obs-959 100 %

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