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- PDB-4dlh: Crystal Structure of the protein Q9HRE7 from Halobacterium salina... -

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Basic information

Entry
Database: PDB / ID: 4dlh
TitleCrystal Structure of the protein Q9HRE7 from Halobacterium salinarium at the resolution 1.9A, Northeast Structural Genomics Consortium (NESG) Target HsR50
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG)
Function / homologyProtein of unknown function DUF1684 / Protein of unknown function (DUF1684) / DUF1684 family protein
Function and homology information
Biological speciesHalobacterium sp. NRC-1 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HsR50
Authors: Kuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)43,1652
Polymers43,1652
Non-polymers00
Water6,071337
1
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,5821
Polymers21,5821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)21,5821
Polymers21,5821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.473, 74.933, 112.987
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,23.9 kD,91.6%

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Components

#1: Protein uncharacterized protein


Mass: 21582.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halobacterium sp. NRC-1 (Halophile) / References: UniProt: Q9HRE7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: mocrobatch under oil / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:KH2PO4 0.1M, HEPES 0.1M, PEG 8000 40%., mocrobatch under oil, temperature 293KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 54970 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 22.33 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 23.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.172 / % possible all: 72.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2LOK

2lok


Resolution: 1.9→38.244 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.856 / SU ML: 0.19 / Cross valid method: throughput / σ(F): 1.34 / Phase error: 21.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1499 5.08 %random
Rwork0.174 ---
obs0.176 29492 96.51 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.96 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso max: 92.83 Å2 / Biso mean: 29.543 Å2 / Biso min: 8.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.729 Å20 Å2-0 Å2
2--3.109 Å2-0 Å2
3----1.379 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 0 337 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072806
X-RAY DIFFRACTIONf_angle_d1.0933838
X-RAY DIFFRACTIONf_chiral_restr0.079403
X-RAY DIFFRACTIONf_plane_restr0.004532
X-RAY DIFFRACTIONf_dihedral_angle_d12.6651000
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9610.2481110.1781962207376
1.961-2.0310.2311450.1792374251992
2.031-2.1130.2521240.172585270999
2.113-2.2090.2461380.1722586272499
2.209-2.3250.2241330.1622590272399
2.325-2.4710.2081270.1722630275799
2.471-2.6620.2671390.19425852724100
2.662-2.930.2581380.19326342772100
2.93-3.3530.2061470.18526412788100
3.353-4.2240.1661570.15626542811100
4.224-38.2520.2111400.1722752289297
Refinement TLS params.Method: refined / Origin x: 25.1288 Å / Origin y: 38.7723 Å / Origin z: 67.8398 Å
111213212223313233
T0.0863 Å2-0.0148 Å2-0.0059 Å2-0.1325 Å2-0.0071 Å2--0.0897 Å2
L0.2463 °2-0.0453 °2-0.0614 °2-0.9652 °2-0.0318 °2--0.3263 °2
S-0.007 Å °0.0085 Å °-0.013 Å °-0.006 Å °0.0141 Å °0.0436 Å °0.0182 Å °-0.0014 Å °-0.0052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA10 - 186
2X-RAY DIFFRACTION1allB11 - 190
3X-RAY DIFFRACTION1allB - A1 - 358

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