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- PDB-2cqz: Crystal Structure of PH0347 protein from Pyrococcus horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 2cqz
TitleCrystal Structure of PH0347 protein from Pyrococcus horikoshii OT3
Components177aa long hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical proteins / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


5'-deoxynucleotidase / 5'-deoxynucleotidase activity
Similarity search - Function
HD domain / 5'-deoxynucleotidase YfbR/HDDC2 / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / 5'-deoxynucleotidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLokanath, N.K. / Terao, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of PH0347 protein from Pyrococcus horikoshii OT3
Authors: Lokanath, N.K. / Terao, Y. / Kunishima, N.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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.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_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: 177aa long hypothetical protein
B: 177aa long hypothetical protein
C: 177aa long hypothetical protein
D: 177aa long hypothetical protein
E: 177aa long hypothetical protein
F: 177aa long hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,10512
Polymers122,7536
Non-polymers3526
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20880 Å2
ΔGint-228 kcal/mol
Surface area38070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.511, 101.166, 78.646
Angle α, β, γ (deg.)90.00, 119.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assemply of this protein is hexamer, which confirmed by DLS experiments

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Components

#1: Protein
177aa long hypothetical protein


Mass: 20458.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): 21-CodonPlus(DE3)-RIL / References: UniProt: O58085
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.3 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 9
Details: Sodium chloride, Bicine, PEG-MME 550, pH 9.0, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 7, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 32523 / Num. obs: 32607 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.69 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XX7

1xx7


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.31 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22531 1616 5 %RANDOM
Rwork0.195 ---
all0.195 32607 --
obs0.195 32523 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.287 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å20 Å2-0.69 Å2
2--3.74 Å20 Å2
3----2.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 6 171 8625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228592
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.98711568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.97351032
X-RAY DIFFRACTIONr_chiral_restr0.10.21320
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026270
X-RAY DIFFRACTIONr_nbd_refined0.2530.24427
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2321
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3320.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.27
X-RAY DIFFRACTIONr_mcbond_it1.0221.55184
X-RAY DIFFRACTIONr_mcangle_it2.03628370
X-RAY DIFFRACTIONr_scbond_it3.51133408
X-RAY DIFFRACTIONr_scangle_it5.834.53198
LS refinement shellResolution: 2.604→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 102
Rwork0.244 2025
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.593-0.1565-0.24341.3741-0.20330.68220.0357-0.16240.16940.0681-0.0014-0.126-0.06610.0765-0.03430.0792-0.0173-0.03970.067-0.05360.14190.500262.364266.7192
21.5224-0.13540.21291.13920.421.7054-0.02930.27730.1106-0.21660.0193-0.0294-0.2462-0.01610.010.1593-0.02050.00420.11210.06310.0371-25.675361.666834.8374
30.51020.38010.05561.5220.6431.4178-0.03530.02210.06240.01040.01410.0819-0.0408-0.28760.02120.04830.02980.02120.13240.00390.0985-40.379561.386873.2762
41.09970.3989-0.0981.48650.39770.9716-0.0322-0.1606-0.04220.21710.0354-0.09630.1709-0.005-0.00320.15840.0082-0.00720.1040.03620.0436-25.326347.355281.9203
50.65870.0018-0.04111.28070.04961.4257-0.0070.0779-0.0347-0.1379-0.02420.13310.1237-0.27780.03120.0859-0.0311-0.04340.14720.00560.0903-40.072846.732943.2094
61.70480.13170.07531.1393-0.50041.1372-0.03730.2113-0.1672-0.08030.0659-0.18480.04250.0461-0.02860.0789-0.00130.03370.0539-0.05490.13930.781547.600850.0351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1724 - 175
2X-RAY DIFFRACTION2BB1 - 1724 - 175
3X-RAY DIFFRACTION3CC1 - 1724 - 175
4X-RAY DIFFRACTION4DD1 - 1724 - 175
5X-RAY DIFFRACTION5EE1 - 1724 - 175
6X-RAY DIFFRACTION6FF1 - 1724 - 175

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