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- PDB-3q4r: Crystal Structure of a deletion mutant(11-185) of hypothetical pr... -

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Basic information

Entry
Database: PDB / ID: 3q4r
TitleCrystal Structure of a deletion mutant(11-185) of hypothetical protein MJ0754 with Zn2+
ComponentsUncharacterized protein MJ0754
KeywordsUNKNOWN FUNCTION / ferritin-like protein / four-helix bundle / metal binding / dinuclear center
Function / homologyDomain of unknown function DUF2202 / Uncharacterized protein domain (DUF2202) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / Uncharacterized protein MJ0754
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Proteins / Year: 2011
Title: Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii.
Authors: Lee, E.H. / Kim, H.S. / Kim, H.Y. / Jeon, Y.H. / Hwang, K.Y.
History
DepositionDec 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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

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Assembly

Deposited unit
A: Uncharacterized protein MJ0754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3474
Polymers22,9341
Non-polymers4133
Water3,063170
1
A: Uncharacterized protein MJ0754
hetero molecules

A: Uncharacterized protein MJ0754
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6948
Polymers45,8682
Non-polymers8266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)52.943, 80.129, 93.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Uncharacterized protein MJ0754


Mass: 22933.805 Da / Num. of mol.: 1 / Fragment: residues 11-185(deletion 1-10) / Mutation: deletion 1-10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: MJ0754 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58164
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / Bis-tris propane


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.17 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-tris propane, 22% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2009
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 24608 / % possible obs: 90.4 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.66146
1.66-1.72172.9
1.72-1.8193.7
1.8-1.9197.6
1.9-2.02198.2
2.02-2.17198.5
2.17-2.39199.1
2.39-2.74198.6
2.74-3.45198.9
3.45-50198.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q4N

3q4n


Resolution: 1.6→32.13 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.923 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1230 5.1 %RANDOM
Rwork0.1835 ---
obs0.1855 24061 90.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 394.28 Å2 / Biso mean: 25.2956 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1406 0 21 170 1597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221449
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9831948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3235169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21626.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89415284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.028155
X-RAY DIFFRACTIONr_chiral_restr0.1580.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211072
X-RAY DIFFRACTIONr_mcbond_it1.3291.5848
X-RAY DIFFRACTIONr_mcangle_it2.33921375
X-RAY DIFFRACTIONr_scbond_it3.9793601
X-RAY DIFFRACTIONr_scangle_it6.5444.5573
LS refinement shellResolution: 1.601→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 48 -
Rwork0.25 789 -
all-837 -
obs--43.46 %

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