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- PDB-2hsb: Crystal structure of a hepn domain containing protein (af_0298) f... -

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Basic information

Entry
Database: PDB / ID: 2hsb
TitleCrystal structure of a hepn domain containing protein (af_0298) from archaeoglobus fulgidus at 1.95 A resolution
ComponentsHypothetical UPF0332 protein AF0298
KeywordsUNKNOWN FUNCTION / Duf103 family / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology: / HEPN domain / HEPN domain / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / UPF0332 protein AF_0298
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_069135.1) from Archaeoglobus Fulgidus at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0332 protein AF0298
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0729
Polymers14,8121
Non-polymers1,2598
Water84747
1
A: Hypothetical UPF0332 protein AF0298
hetero molecules

A: Hypothetical UPF0332 protein AF0298
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,14318
Polymers29,6252
Non-polymers2,51916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4060 Å2
ΔGint-78 kcal/mol
Surface area12380 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.665, 60.665, 80.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-126-

SO4

21A-176-

HOH

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Components

#1: Protein Hypothetical UPF0332 protein AF0298


Mass: 14812.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: NP_069135.1 / Production host: Escherichia coli (E. coli) / References: UniProt: O29944
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.32 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 277 K / pH: 7
Details: 0.05M Li2SO4, 50.0% PEG-200, 0.1M TRIS, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 17, 2006 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979361
30.979181
ReflectionResolution: 1.9→29.336 Å / Num. obs: 11515 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 14.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.925 / Mean I/σ(I) obs: 2 / Rsym value: 0.925 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHARPphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→29.34 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.819 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. SO4 AND PEG-200 (PG4) MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 4. OCCUPANCIES OF SO4 1 AND PG4 7 ARE REDUCED BECAUSE THEY LIE ON SPECIAL POSITIONS. 5. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 552 4.8 %RANDOM
Rwork0.184 ---
obs0.186 11471 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 64 47 1131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221102
X-RAY DIFFRACTIONr_bond_other_d0.0020.02810
X-RAY DIFFRACTIONr_angle_refined_deg1.2752.0181456
X-RAY DIFFRACTIONr_angle_other_deg0.87231966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5215129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55223.84652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85715212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.019159
X-RAY DIFFRACTIONr_chiral_restr0.0730.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021160
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
X-RAY DIFFRACTIONr_nbd_refined0.2160.2240
X-RAY DIFFRACTIONr_nbd_other0.1790.2752
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2527
X-RAY DIFFRACTIONr_nbtor_other0.0840.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1343685
X-RAY DIFFRACTIONr_mcbond_other0.453260
X-RAY DIFFRACTIONr_mcangle_it2.91351000
X-RAY DIFFRACTIONr_scbond_it5.1668521
X-RAY DIFFRACTIONr_scangle_it6.64411454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 39 -
Rwork0.231 778 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 39.633 Å / Origin y: 32.735 Å / Origin z: 29.261 Å
111213212223313233
T-0.0942 Å20.0028 Å20.0267 Å2--0.1271 Å2-0.0123 Å2---0.2359 Å2
L0.1272 °2-0.232 °2-0.4838 °2-0.4426 °20.9055 °2--2.7724 °2
S0.0557 Å °-0.0296 Å °-0.0486 Å °-0.1992 Å °0.023 Å °-0.0219 Å °-0.2199 Å °0.0791 Å °-0.0787 Å °

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