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- PDB-1rlh: Structure of a conserved protein from Thermoplasma acidophilum -

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Basic information

Entry
Database: PDB / ID: 1rlh
TitleStructure of a conserved protein from Thermoplasma acidophilum
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / T. acidophilum / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Ta1353-like / Ta1353-like / Adenosine specific kinase / Ta1353-like superfamily / Adenosine specific kinase / hypothetical protein tt1634 / Complement Module; domain 1 / Ribbon / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, Molecular replacement / Resolution: 1.8 Å
AuthorsCuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of a conserved protein from T. acidophilum
Authors: Cuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1402
Polymers19,1171
Non-polymers231
Water4,288238
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4196
Polymers57,3503
Non-polymers693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9200 Å2
ΔGint-55 kcal/mol
Surface area18600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.329, 74.329, 50.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-522-

NA

21A-567-

HOH

DetailsThe biologically assembly unknown, but monomer forms a very tight trimer in two crystal forms

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Components

#1: Protein conserved hypothetical protein


Mass: 19116.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: CAC12474 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HII6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium acetate, NaCl, PEG 3350, glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21501
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0332
SYNCHROTRONAPS 19-ID20.97964,0.97951,0.96411
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDJul 15, 2002
CUSTOM-MADE2CCDNov 17, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1sagitally focused Si(111)SINGLE WAVELENGTHMx-ray1
2sagitally focused Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.03321
20.979641
30.979511
40.964111
ReflectionResolution: 1.75→39.9 Å / Num. all: 14981 / Num. obs: 14981 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.9 Å2 / Limit h max: 35 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 1102536.72 / Observed criterion F min: 6.6

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data collection
HKL-2000data reduction
SHARPphasing
MOLREPphasing
CNS1.1refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD, Molecular replacement / Resolution: 1.8→39.9 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 0.33 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 715 5 %RANDOM
Rwork0.179 ---
all0.1987 14946 --
obs0.196 14321 95.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 69.2453 Å2 / ksol: 0.373886 e/Å3
Displacement parametersBiso max: 70.44 Å2 / Biso mean: 30.27 Å2 / Biso min: 11.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-0.16 Å20 Å2
2---1.17 Å20 Å2
3---2.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1159 0 1 238 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_d1.2
X-RAY DIFFRACTIONx_torsion_deg24.6
X-RAY DIFFRACTIONx_torsion_impr_deg0.66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.3615640.29513370.0481864139374.7
1.88-1.980.241995.80.23415950.0241827169492.7
1.98-2.110.192995.30.18317630.0191869186299.6
2.11-2.270.239965.20.18617670.0241869186399.7
2.27-2.50.239774.10.18517890.0271867186699.9
2.5-2.860.2291035.50.16617730.02318761876100
2.86-3.60.169985.20.15717720.01718701870100
3.6-39.90.192874.60.17218100.0211921189798.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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