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- PDB-1o5j: Crystal structure of Periplasmic divalent cation tolerance protei... -

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Basic information

Entry
Database: PDB / ID: 1o5j
TitleCrystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution
Componentsperiplasmic divalent cation tolerance protein
KeywordsUNKNOWN FUNCTION / TM1056 / PERIPLASMIC DIVALENT CATION TOLERANCE PROTEIN / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


response to metal ion / copper ion binding / cytoplasm
Similarity search - Function
: / Divalent ion tolerance protein, CutA / CutA1 divalent ion tolerance protein / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Divalent-cation tolerance protein CutA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Periplasmic divalent cation tolerance protein (TM1056) from Thermotoga maritima at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: 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 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: periplasmic divalent cation tolerance protein


Theoretical massNumber of molelcules
Total (without water)13,7491
Polymers13,7491
Non-polymers00
Water1,33374
1
A: periplasmic divalent cation tolerance protein

A: periplasmic divalent cation tolerance protein

A: periplasmic divalent cation tolerance protein


Theoretical massNumber of molelcules
Total (without water)41,2463
Polymers41,2463
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area6570 Å2
ΔGint-44 kcal/mol
Surface area13600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.514, 52.514, 34.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-127-

HOH

21A-140-

HOH

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Components

#1: Protein periplasmic divalent cation tolerance protein


Mass: 13748.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0E6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.05 Å3/Da / Density % sol: 39.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 10.5
Details: 30% PEG-400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97944, 0.97924, 0.95658
DetectorType: APS / Detector: CCD / Date: Oct 25, 2002
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
10.979441
20.979241
30.956581
ReflectionResolution: 1.95→45.48 Å / Num. obs: 7337 / % possible obs: 100 % / Redundancy: 7.49 % / Biso Wilson estimate: 41.58 Å2 / Rsym value: 0.068 / Net I/σ(I): 32.91
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.99 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 563 / Rsym value: 0.245 / % possible all: 70.02

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→45.48 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.47 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22061 339 4.6 %RANDOM
Rwork0.15603 ---
obs0.15907 6993 93.94 %-
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: 39.27 Å2
Baniso -1Baniso -2Baniso -3
1--2.39 Å2-1.2 Å20 Å2
2---2.39 Å20 Å2
3---3.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms890 0 0 74 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022914
X-RAY DIFFRACTIONr_bond_other_d0.0020.02828
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9381235
X-RAY DIFFRACTIONr_angle_other_deg0.80431928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3615103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30723.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60915172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.559155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02193
X-RAY DIFFRACTIONr_nbd_refined0.2060.2180
X-RAY DIFFRACTIONr_nbd_other0.1930.2796
X-RAY DIFFRACTIONr_nbtor_other0.0890.2553
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.211
X-RAY DIFFRACTIONr_mcbond_it2.5113625
X-RAY DIFFRACTIONr_mcangle_it3.1165843
X-RAY DIFFRACTIONr_scbond_it5.6928466
X-RAY DIFFRACTIONr_scangle_it7.13311392
LS refinement shellResolution: 1.95→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 19 5.07 %
Rwork0.225 356 -
Refinement TLS params.Method: refined / Origin x: -8.464 Å / Origin y: 52.935 Å / Origin z: 24.378 Å
111213212223313233
T-0.1697 Å2-0.0176 Å20.0042 Å2--0.1922 Å20.0569 Å2---0.1708 Å2
L4.7897 °2-1.0135 °2-0.8635 °2-2.8242 °20.3902 °2--1.5748 °2
S0.0623 Å °-0.328 Å °-0.374 Å °0.1637 Å °-0.0623 Å °0.3014 Å °0.1072 Å °-0.1999 Å °0 Å °
Refinement TLS groupSelection: ALL

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