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- PDB-4ipa: Structure of a thermophilic Arx1 -

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Basic information

Entry
Database: PDB / ID: 4ipa
TitleStructure of a thermophilic Arx1
ComponentsPutative curved DNA-binding protein
KeywordsHYDROLASE / MAP / Methionine Aminopeptidase / Ribosome biogenesis
Function / homology
Function and homology information


: / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative curved DNA-binding protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBange, G. / Sinning, I.
CitationJournal: BMC Evol Biol / Year: 2013
Title: Consistent mutational paths predict eukaryotic thermostability.
Authors: van Noort, V. / Bradatsch, B. / Arumugam, M. / Amlacher, S. / Bange, G. / Creevey, C. / Falk, S. / Mende, D.R. / Sinning, I. / Hurt, E. / Bork, P.
History
DepositionJan 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative curved DNA-binding protein
B: Putative curved DNA-binding protein
C: Putative curved DNA-binding protein
D: Putative curved DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,44511
Polymers186,7734
Non-polymers6727
Water16,250902
1
A: Putative curved DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8853
Polymers46,6931
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative curved DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7892
Polymers46,6931
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative curved DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8853
Polymers46,6931
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative curved DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8853
Polymers46,6931
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)191.998, 193.316, 70.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Putative curved DNA-binding protein


Mass: 46693.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0023380 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2 / References: UniProt: G0S4S7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithiumacetate, 2.2M Amminiumsulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.3→86.4 Å / Num. all: 118103 / Num. obs: 118103 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 13.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4 / Num. unique all: 17031 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q8K

2q8k


Resolution: 2.3→57.176 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 21.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 5918 5.02 %RANDOM
Rwork0.1994 ---
obs0.2013 117991 99.98 %-
all-0 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.486 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4208 Å20 Å20 Å2
2---0.0825 Å2-0 Å2
3---0.5033 Å2
Refinement stepCycle: LAST / Resolution: 2.3→57.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11511 0 35 902 12448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811724
X-RAY DIFFRACTIONf_angle_d1.07215847
X-RAY DIFFRACTIONf_dihedral_angle_d15.074485
X-RAY DIFFRACTIONf_chiral_restr0.0691825
X-RAY DIFFRACTIONf_plane_restr0.0052035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.28285790.218611079X-RAY DIFFRACTION100
2.3822-2.47760.26545530.20611098X-RAY DIFFRACTION100
2.4776-2.59030.26375680.212311105X-RAY DIFFRACTION100
2.5903-2.72690.26785670.211511172X-RAY DIFFRACTION100
2.7269-2.89770.25466270.199211048X-RAY DIFFRACTION100
2.8977-3.12150.23755850.206411174X-RAY DIFFRACTION100
3.1215-3.43560.24415920.205211175X-RAY DIFFRACTION100
3.4356-3.93260.2185950.186711251X-RAY DIFFRACTION100
3.9326-4.95420.21796190.178111289X-RAY DIFFRACTION100
4.9542-57.19360.21726330.209211682X-RAY DIFFRACTION100

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