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- PDB-1p8c: Crystal structure of TM1620 (APC4843) from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1p8c
TitleCrystal structure of TM1620 (APC4843) from Thermotoga maritima
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Conserved hypothetical protein / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


peroxiredoxin activity / oxidoreductase activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKim, Y. / Joachimiak, A. / Brunzelle, J.S. / Korolev, S.V. / Edwards, A. / Xu, X. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure Analysis of Thermotoga maritima protein TM1620 (APC4843)
Authors: Kim, Y. / Joachimiak, A. / Brunzelle, J.S. / Korolev, S.V. / Edwards, A. / Xu, X. / Savchenko, A.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAINS. 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
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)99,1436
Polymers99,1436
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19520 Å2
ΔGint-154 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.819, 82.541, 135.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
conserved hypothetical protein / TM1620 (APC4843)


Mass: 16523.871 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1V5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: potassium citrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97942
SYNCHROTRONAPS 19-ID20.97945, 0.97952, 0.954
Detector
TypeIDDetectorDateDetails
SBC-21CCDSep 2, 2002mirror
SBC-22CCDNov 10, 2002mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979451
30.979521
40.9541
ReflectionResolution: 2.15→50 Å / Num. all: 39155 / Num. obs: 39155 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3655 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
d*TREKdata reduction
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPV. 6.0model building
RefinementMethod to determine structure: SAD / Resolution: 2.3→48.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 153151.96 / Data cutoff high rms absF: 153151.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3051 10 %RANDOM
Rwork0.225 ---
all0.2311 30380 --
obs0.225 30380 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.7314 Å2 / ksol: 0.329463 e/Å3
Displacement parametersBiso mean: 62.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---5.72 Å20 Å2
3---4.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5548 0 0 87 5635
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.961.5
X-RAY DIFFRACTIONc_mcangle_it11.072
X-RAY DIFFRACTIONc_scbond_it9.972
X-RAY DIFFRACTIONc_scangle_it152.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 460 10.7 %
Rwork0.296 3827 -
obs--78.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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