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- PDB-3npg: Crystal structure of a protein with unknown function from DUF364 ... -

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Basic information

Entry
Database: PDB / ID: 3npg
TitleCrystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution
Componentsuncharacterized DUF364 family protein
KeywordsUNKNOWN FUNCTION / protein with unknown function from DUF364 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyPutative heavy-metal chelation domain / Domain of unknown function DUF4213 / Putative heavy-metal chelation / Putative heavy-metal chelation / ACETATE ION / Heavy-metal chelation domain-containing protein
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a protein with unknown function from DUF364 family (PH1506) from PYROCOCCUS HORIKOSHII at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized DUF364 family protein
B: uncharacterized DUF364 family protein
C: uncharacterized DUF364 family protein
D: uncharacterized DUF364 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1608
Polymers113,9244
Non-polymers2364
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint-49 kcal/mol
Surface area36220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.541, 95.179, 159.098
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
uncharacterized DUF364 family protein / uncharacterized protein PH1506


Mass: 28480.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1506 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O59175
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.3000M ammonium acetate, 24.0000% polyethylene glycol 3350, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 7, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91162 Å / Relative weight: 1
ReflectionResolution: 2.7→95.346 Å / Num. obs: 31874 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.245 / Rsym value: 0.245 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.775.10.9810.81182823070.981100
2.77-2.855.10.8940.81160822580.894100
2.85-2.935.10.77411109221720.774100
2.93-3.025.10.691.11101121500.69100
3.02-3.125.10.5761.31068620880.576100
3.12-3.235.10.4991.51028220050.499100
3.23-3.355.10.3961.8989219420.396100
3.35-3.495.10.3322.2946818560.332100
3.49-3.645.10.2662.6924318190.266100
3.64-3.8250.2173.2868317280.217100
3.82-4.0250.1793.8823416390.179100
4.02-4.2750.1474.5773115540.147100
4.27-4.564.90.1275726814770.127100
4.56-4.934.90.1264.8677913770.126100
4.93-5.44.90.1294.8629312830.129100
5.4-6.044.90.1275570011620.127100
6.04-6.974.90.1125.6499310250.112100
6.97-8.544.70.0866.642318920.086100
8.54-12.074.50.0687.232187120.068100
12.07-95.3540.0765.316964280.07699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.2.21data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
Rosettaphasing
PHASERphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: molecular replacement
Starting model: 3l5o

3l5o


Resolution: 2.7→95.346 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.868 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ACETATE (ACT) FROM THE CRYSTALLIZATION CONDITIONS IS MODELED INTO THE STRUCTURE 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1606 5.05 %RANDOM
Rwork0.204 ---
obs0.206 31792 --
Displacement parametersBiso max: 108.74 Å2 / Biso mean: 38.54 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--6.284 Å20 Å20 Å2
2---2.25 Å20 Å2
3---8.533 Å2
Refinement stepCycle: LAST / Resolution: 2.7→95.346 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7541 0 16 52 7609
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2673SINUSOIDAL5
X-RAY DIFFRACTIONt_trig_c_planes179HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1086HARMONIC5
X-RAY DIFFRACTIONt_it7671HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1073SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9004SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7671HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg10405HARMONIC60.52
X-RAY DIFFRACTIONt_omega_torsion2.83
X-RAY DIFFRACTIONt_other_torsion14.97
LS refinement shellResolution: 2.7→2.79 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.25 144 5.05 %
Rwork0.224 2710 -
all0.225 2854 -
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)
10.79150.1480.45760.8989-0.06531.09680.0379-0.03350.0106-0.0184-0.0727-0.0096-0.0455-0.08160.0347-0.13520.00620.0470.0127-0.0051-0.033215.03789.4438154.113
21.37160.6726-0.64940.93990.00272.40440.0285-0.003-0.0333-0.07360.0046-0.07380.01370.1651-0.033-0.21570.0312-0.0296-0.0213-0.0196-0.015646.66376.4436142.739
30.55250.1416-0.65881.64040.49732.80530.05640.03670.1583-0.0401-0.07510.0885-0.2716-0.1040.0187-0.17440.09160.0254-0.05310.0426-0.032613.62928.802125.38
40.8971-0.48250.44441.54910.1741.0394-0.05580.0595-0.0566-0.02910.1056-0.0194-0.0004-0.0251-0.0497-0.15670.00320.03830.0136-0.0641-0.055428.16310.4051113.814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A0 - 248
2X-RAY DIFFRACTION2{ B|* }B4 - 248
3X-RAY DIFFRACTION3{ C|* }C3 - 248
4X-RAY DIFFRACTION4{ D|* }D4 - 248

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