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- PDB-1j31: Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 1j31
TitleCrystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii
ComponentsHypothetical protein PH0642
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta-beta-alpha sandwich
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Similarity search - Function
: / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CN hydrolase domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsSakai, N. / Tajika, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution.
Authors: Sakai, N. / Tajika, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionJan 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein PH0642
B: Hypothetical protein PH0642
C: Hypothetical protein PH0642
D: Hypothetical protein PH0642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,9278
Polymers120,6914
Non-polymers2364
Water11,566642
1
A: Hypothetical protein PH0642
B: Hypothetical protein PH0642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4634
Polymers60,3452
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-26 kcal/mol
Surface area17990 Å2
MethodPISA
2
C: Hypothetical protein PH0642
D: Hypothetical protein PH0642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4634
Polymers60,3452
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-23 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.037, 89.021, 77.871
Angle α, β, γ (deg.)90.00, 96.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein PH0642


Mass: 30172.670 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH0642 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: O58376
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 642 / 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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.1M Sodium acetate, 45% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 4.10
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMsodium acetate1droppH4.1
322.5 %MPD1drop
4100 mMsodium acetate1reservoirpH4.1
545 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9789, 0.9791, 0.9798
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2002
RadiationMonochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97911
30.97981
ReflectionResolution: 1.6→30 Å / Num. obs: 133189 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Biso Wilson estimate: 26.32 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.073 / Net I/σ(I): 6.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.331 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 23.3 Å / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Num. measured all: 601635 / Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.6 % / Redundancy: 4.3 % / Num. unique obs: 19379 / Num. measured obs: 83595 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.194 13282 -RANDOM
Rwork0.166 ---
obs0.166 132614 99.4 %-
all-132614 --
Solvent computationSolvent model: THROUGHOUT / Bsol: 74.7 Å2 / ksol: 0.5 e/Å3
Displacement parametersBiso mean: 15.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.109 Å20 Å2-0.263 Å2
2---1.451 Å20 Å2
3---1.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8412 0 16 642 9070
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.76
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.84
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.436
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.559
X-RAY DIFFRACTIONc_scangle_it3.571
Refine LS restraints NCSNCS model details: RESTRAIN / Weight Biso : 2 / Weight position: 200
LS refinement shellResolution: 1.6→1.67 Å
RfactorNum. reflection% reflection
Rfree0.241 1657 -
Rwork0.2254 --
obs--97.7 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.84
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.241

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