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- PDB-2hq4: Crystal Structure of ORF 1580 a hypothetical protein from Pyrococ... -

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Basic information

Entry
Database: PDB / ID: 2hq4
TitleCrystal Structure of ORF 1580 a hypothetical protein from Pyrococcus horikoshii
ComponentsHypothetical protein PH1570
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Singleton Protein / PH1580 / PSI SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / Protein Structure Initiative
Function / homologyPH1570-like fold / PH1570-like / PH1570-like domain / PH1570-like superfamily / Ph1570 protein / 3-Layer(aba) Sandwich / Alpha Beta / PH1570-like domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsLi, Y. / Marshall, M. / Chang, J. / Zhao, M. / Zhang, M. / Xu, H. / Liu, Z.J. / Rose, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of ORF 1580 a hypothetical protein from Pyrococcus horikoshii
Authors: Li, Y. / Marshall, M. / Chang, J. / Zhao, M. / Zhang, M. / Xu, H. / LIU, Z.J. / ROSE, J.P. / Wang, B.C. / Southeast Collaboratory for Structural Genomics (SECSG)
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 13, 2017Group: Refinement description / Category: refine / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_ncs_dom_lim / 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_related.db_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.6Oct 22, 2025Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PH1570
B: Hypothetical protein PH1570


Theoretical massNumber of molelcules
Total (without water)38,6792
Polymers38,6792
Non-polymers00
Water3,855214
1
A: Hypothetical protein PH1570


Theoretical massNumber of molelcules
Total (without water)19,3391
Polymers19,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein PH1570


Theoretical massNumber of molelcules
Total (without water)19,3391
Polymers19,3391
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.869, 46.392, 94.750
Angle α, β, γ (deg.)90.00, 132.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 4 / Auth seq-ID: -8 - 152 / Label seq-ID: 1 - 161

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hypothetical protein PH1570


Mass: 19339.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O59278
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (12 mg/ml) AND RESERVOIR SOLUTION CONTAINinG 0.2M ammonium dihydrogen phosphate, 20% W/V ...Details: HANGING DROP VAPOR DIFFUSION USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (12 mg/ml) AND RESERVOIR SOLUTION CONTAINinG 0.2M ammonium dihydrogen phosphate, 20% W/V PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2006 / Details: Rosenbaum
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9791
ReflectionResolution: 1.99→70 Å / Num. all: 29575 / Num. obs: 28050 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rsym value: 0.075 / Net I/σ(I): 11.6
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 4.6 % / Rsym value: 0.293 / % possible all: 92.3

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Processing

Software
NameVersionClassification
Sca2Structuremodel building
REFMAC5.2.0019refinement
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SCA2STRUCTUREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.356 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23184 1491 5.1 %RANDOM
Rwork0.19456 ---
obs0.19654 28017 98.89 %-
all-28050 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å2-0.44 Å2
2--0.63 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2689 0 0 214 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222756
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.9773700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5835313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03125.108139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74415534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.648158
X-RAY DIFFRACTIONr_chiral_restr0.1350.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022070
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.21206
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21858
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2370.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.51650
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.91922542
X-RAY DIFFRACTIONr_scbond_it2.89131327
X-RAY DIFFRACTIONr_scangle_it4.2984.51158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1328 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.620.5
medium thermal1.252
LS refinement shellResolution: 1.988→2.039 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 106 -
Rwork0.22 1825 -
obs--89.48 %

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