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- PDB-2it1: Structure of PH0203 protein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2it1
TitleStructure of PH0203 protein from Pyrococcus horikoshii
Components362aa long hypothetical maltose/maltodextrin transport ATP-binding protein
KeywordsTRANSPORT PROTEIN / ATP binding protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
MalK, OB fold domain / MalK OB fold domain / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...MalK, OB fold domain / MalK OB fold domain / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Nucleic acid-binding proteins / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
362aa long hypothetical maltose/maltodextrin transport ATP-binding protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsLokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of PH0203 protein from Pyrococcus horikoshii
Authors: Lokanath, N.K. / Kunishima, N.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 362aa long hypothetical maltose/maltodextrin transport ATP-binding protein
B: 362aa long hypothetical maltose/maltodextrin transport ATP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8313
Polymers81,7352
Non-polymers961
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.230, 85.319, 82.598
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 362aa long hypothetical maltose/maltodextrin transport ATP-binding protein


Mass: 40867.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon Plus (DE3)-RIL / References: UniProt: O57942
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.1
Details: 20% PEG 4000, 0.5M LI2SO4, pH 8.1, microbatch, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B111
SYNCHROTRONSPring-8 BL26B120.979103, 0.9794, 1.0
Detector
TypeIDDetectorDate
RIGAKU RAXIS V1IMAGE PLATEOct 12, 2006
RIGAKU RAXIS V2IMAGE PLATEApr 16, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITEMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9791031
30.97941
ReflectionResolution: 1.94→50 Å / Num. all: 47216 / Num. obs: 46653 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.9
Reflection shellResolution: 1.94→2.01 Å / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.94→20 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.788 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2494 5.1 %RANDOM
Rwork0.21 ---
obs0.21 46653 98.14 %-
all-47216 --
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: 29.143 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å22.5 Å2
2--0.76 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.94→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 5 375 6134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225868
X-RAY DIFFRACTIONr_bond_other_d0.0010.024106
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9957926
X-RAY DIFFRACTIONr_angle_other_deg0.846310099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7975721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.15324.96250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.421151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.951528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026357
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
X-RAY DIFFRACTIONr_nbd_refined0.2130.21132
X-RAY DIFFRACTIONr_nbd_other0.1950.24065
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22806
X-RAY DIFFRACTIONr_nbtor_other0.0860.23214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.261
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.232
X-RAY DIFFRACTIONr_mcbond_it1.1481.54709
X-RAY DIFFRACTIONr_mcbond_other0.1721.51458
X-RAY DIFFRACTIONr_mcangle_it1.29125852
X-RAY DIFFRACTIONr_scbond_it1.95232635
X-RAY DIFFRACTIONr_scangle_it2.7014.52074
LS refinement shellResolution: 1.941→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 165 -
Rwork0.255 2956 -
obs--85.88 %

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