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- PDB-1vjx: Crystal structure of a putative ferritin-like diiron-carboxylate ... -

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Basic information

Entry
Database: PDB / ID: 1vjx
TitleCrystal structure of a putative ferritin-like diiron-carboxylate protein (tm1526) from thermotoga maritima at 2.30 A resolution
Componentsputative ferritin-like diiron-carboxylate protein TM1526
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Rubrerythrin, diiron-binding domain / Rubrerythrin / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rubrerythrin diiron-binding domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative ferritin-like diiron-carboxylate protein (TM1526) from Thermotoga maritima at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative ferritin-like diiron-carboxylate protein TM1526


Theoretical massNumber of molelcules
Total (without water)18,8221
Polymers18,8221
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.333, 82.333, 121.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

#1: Protein putative ferritin-like diiron-carboxylate protein TM1526


Mass: 18821.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1526 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1L2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.8 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: Phosphate Citrate pH 4.2, 10% 2-propanol, 0.2M Li2SO4 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979292, 0.964063, 0.979127
DetectorType: APS-1 / Detector: CCD / Date: Feb 20, 2004
Details: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792921
20.9640631
30.9791271
ReflectionResolution: 2.3→50 Å / Num. obs: 9150 / % possible obs: 94.75 % / Redundancy: 8.82 % / Biso Wilson estimate: 51.21 Å2 / Rsym value: 0.077 / Net I/σ(I): 22.69
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.45 / Num. unique all: 897 / Rsym value: 0.681 / % possible all: 95.43

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
REFMAC5.2.0000refinement
RefinementMethod to determine structure: MAD / Resolution: 2.3→42.06 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 16.424 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.241
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25652 596 6.5 %RANDOM
Rwork0.21727 ---
obs0.21979 8537 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.678 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--1.79 Å20 Å2
3----3.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1242 0 0 60 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211274
X-RAY DIFFRACTIONr_bond_other_d0.0020.021160
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.961711
X-RAY DIFFRACTIONr_angle_other_deg0.82932704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03424.34869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.39815256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7841510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021401
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02260
X-RAY DIFFRACTIONr_nbd_refined0.2230.2293
X-RAY DIFFRACTIONr_nbd_other0.1750.21180
X-RAY DIFFRACTIONr_nbtor_other0.0890.2747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.23
X-RAY DIFFRACTIONr_mcbond_it0.9661.5822
X-RAY DIFFRACTIONr_mcbond_other0.1861.5302
X-RAY DIFFRACTIONr_mcangle_it1.23421208
X-RAY DIFFRACTIONr_scbond_it2.0723572
X-RAY DIFFRACTIONr_scangle_it3.2164.5503
LS refinement shellResolution: 2.299→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 48 7.26 %
Rwork0.301 613 -
Refinement TLS params.Method: refined / Origin x: 47.7894 Å / Origin y: 50.5616 Å / Origin z: 36.5663 Å
111213212223313233
T-0.371 Å2-0.0545 Å2-0.0112 Å2-0.1343 Å20.0473 Å2---0.1272 Å2
L3.5622 °2-1.0395 °21.5676 °2-2.3972 °2-1.5394 °2--4.7034 °2
S-0.1497 Å °0.3413 Å °0.3096 Å °-0.081 Å °-0.0064 Å °-0.1317 Å °-0.2842 Å °0.0452 Å °0.1561 Å °
Refinement TLS groupSelection: ALL

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