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- PDB-2e6u: Crystal structure of hypothetical protein PH1109 from Pyrococcus ... -

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Basic information

Entry
Database: PDB / ID: 2e6u
TitleCrystal structure of hypothetical protein PH1109 from Pyrococcus horikoshii
Componentshypothetical protein PH1109
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Rossmann-like / CoA binding / Structural Genomics Consortium for Research on Gene Expression System
Function / homology
Function and homology information


CoA binding domain / CoA binding domain / CoA-binding / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / CoA-binding domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKitago, Y. / Min, Y. / Watanabe, N. / Tanaka, I.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2005
Title: Structure determination of a novel protein by sulfur SAD using chromium radiation in combination with a new crystal-mounting method
Authors: Kitago, Y. / Watanabe, N. / Tanaka, I.
History
DepositionJan 3, 2007Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 23, 2007ID: 2CZZ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Mar 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_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_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_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_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
X: hypothetical protein PH1109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6616
Polymers16,7471
Non-polymers9145
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
X: hypothetical protein PH1109
hetero molecules

X: hypothetical protein PH1109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,32312
Polymers33,4952
Non-polymers1,82810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_556-x,-x+y,-z+4/31
Buried area4080 Å2
ΔGint-66 kcal/mol
Surface area14570 Å2
MethodPISA
3
X: hypothetical protein PH1109
hetero molecules

X: hypothetical protein PH1109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,32312
Polymers33,4952
Non-polymers1,82810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area5730 Å2
ΔGint-55 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.563, 69.563, 142.606
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11X-203-

CL

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Components

#1: Protein hypothetical protein PH1109


Mass: 16747.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PH1109 / Plasmid: pET-26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58836
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% (v/v) PEG 300, 0.1M Cacodylate buffer pH6.5, 0.2M Calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2004 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 19648 / Num. obs: 19648 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 21.426 Å2 / Rsym value: 0.073 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 1905 / Rsym value: 0.458 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.934 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23305 999 5.1 %RANDOM
Rwork0.20536 ---
obs0.20668 18565 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2816 Å0.2625 Å
Luzzati d res low-5 Å
Luzzati sigma a0.0962 Å0.1179 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1155 0 52 45 1252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0391663
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4625141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48624.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06915227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.182159
X-RAY DIFFRACTIONr_chiral_restr0.1520.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.2512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2812
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2890.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.010.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9521.5732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65121155
X-RAY DIFFRACTIONr_scbond_it2.6763567
X-RAY DIFFRACTIONr_scangle_it4.114.5508
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 65 -
Rwork0.227 1307 -
obs--100 %

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