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- PDB-2p9x: Crystal structure of PH0832 from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2p9x
TitleCrystal structure of PH0832 from Pyrococcus horikoshii OT3
ComponentsHypothetical protein PH0832
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrococcus horikoshii OT3 / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Protein of unknown function DUF3227 / Nitrosopumilus output domain 5 / Nitrosopumilus output domain 5-like superfamily / Nitrosopumilus output domain 5 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Nitrosopumilus output domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsSugahara, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of PH0832 from Pyrococcus horikoshii OT3
Authors: Sugahara, M. / Kunishima, N.
History
DepositionMar 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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_atom_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_asym_id / _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_atom_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_asym_id / _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_asym_id / _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_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: Hypothetical protein PH0832
B: Hypothetical protein PH0832
C: Hypothetical protein PH0832
D: Hypothetical protein PH0832
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50710
Polymers44,1274
Non-polymers3806
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-129 kcal/mol
Surface area17400 Å2
MethodPISA, PQS
2
A: Hypothetical protein PH0832
D: Hypothetical protein PH0832
hetero molecules

B: Hypothetical protein PH0832
C: Hypothetical protein PH0832
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50710
Polymers44,1274
Non-polymers3806
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area4960 Å2
ΔGint-148 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.357, 65.870, 104.050
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
Hypothetical protein PH0832


Mass: 11031.775 Da / Num. of mol.: 4 / Fragment: UNP residues 11-109
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58562
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 295 K / Method: oil-micro batch / pH: 5.8
Details: 10% isopropanol, 0.1M cacodylate, 0.2M zinc acetate, pH 5.8, oil-micro batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 52277 / Num. obs: 52277 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24.94 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.053 / Net I/σ(I): 10.9
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5164 / Rsym value: 0.579 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→19.97 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2591 -RANDOM
Rwork0.219 ---
obs0.219 52201 99.8 %-
all-52201 --
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å20 Å2
2---3.19 Å20 Å2
3----0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 12 400 3453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.005
X-RAY DIFFRACTIONc_bond_d1.1
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.311 279 -
Rwork0.296 --
obs-4864 99.6 %

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