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- PDB-27af: Crystal structure of protein PF1862 from Pyrococcus furiosus crys... -

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Basic information

Entry
Database: PDB / ID: 27af
TitleCrystal structure of protein PF1862 from Pyrococcus furiosus crystallized at 04 degree Celsius
ComponentsDNA-binding protein
KeywordsDNA BINDING PROTEIN / Nucleic acid-binding protein / Protein of unknown function (DUF655)
Function / homologyProtein of unknown function DUF655 / Protein of unknown function (DUF655) / Nucleic acid-binding, OB-fold / DNA binding / DNA-binding protein
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsShubhangi, S. / Gaikwad, S.S. / Taneja, S.S. / Baig, S. / Palasiyawala, K. / Kumar, A. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
Citation
Journal: To Be Published
Title: Crystal structure of PF1862 protein from Pyrococcus furiosus crystallized at 04 degree Celsius
Authors: Shubhangi, S. / Gaikwad, S.S. / Taneja, S.S. / Baig, S. / Palasiyawala, K. / Kumar, A. / Makde, R.D.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 22, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0563
Polymers21,9861
Non-polymers712
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-18 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.483, 39.574, 64.933
Angle α, β, γ (deg.)90.000, 100.532, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DNA-binding protein


Mass: 21985.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Strain: DSM 3638 / Gene: PF1862 / Plasmid: pST50Trc2STRHISN / Details (production host): Tan Lab USA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS / References: UniProt: Q8TZW3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: 0.1 M Bis-Tris (pH 5.5) and 17% PEG 10000; protein PF1862 at 20 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.997 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 8, 2026 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.52→39.57 Å / Num. obs: 29688 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.095 / Net I/σ(I): 11.4
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2 / Num. unique obs: 1345 / CC1/2: 0.927 / Rpim(I) all: 0.213 / Rrim(I) all: 0.546 / % possible all: 92.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.52→35.52 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 23.1763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2199 1298 4.75 %
Rwork0.1841 26000 -
obs0.1857 27298 91.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.99 Å2
Refinement stepCycle: LAST / Resolution: 1.52→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 2 260 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121513
X-RAY DIFFRACTIONf_angle_d1.14222036
X-RAY DIFFRACTIONf_chiral_restr0.0742220
X-RAY DIFFRACTIONf_plane_restr0.0121260
X-RAY DIFFRACTIONf_dihedral_angle_d16.076599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.580.26981250.26132554X-RAY DIFFRACTION81.75
1.58-1.650.30421330.24052676X-RAY DIFFRACTION85.54
1.65-1.740.25531270.21682727X-RAY DIFFRACTION87.09
1.74-1.850.21721440.20872815X-RAY DIFFRACTION89.45
1.85-1.990.29761540.212919X-RAY DIFFRACTION93.26
1.99-2.190.2411560.19372935X-RAY DIFFRACTION93.78
2.19-2.510.19691430.18833034X-RAY DIFFRACTION95.64
2.51-3.160.21831630.19033088X-RAY DIFFRACTION98.01
3.16-35.520.18741530.15023252X-RAY DIFFRACTION99.33
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)
12.901279099620.310520654139-0.201568574575.885508314980.5740329447685.61290533952-0.04128305063190.1477867644450.172242554846-0.03191686715130.1641274398390.365421656409-0.436461345602-0.103911849651-0.08686093270730.124995070604-0.0334120100163-0.01463127434350.1386660585390.03047218484720.11277881690718.23340822416.6556840265511.4341276663
23.492340101350.253456404706-0.6887576603612.04629421552-0.6650696259662.439763854830.04168973345320.1823335115670.149961802713-0.0135328526397-0.00472841145369-0.14112110696-0.3130449127040.254663873602-0.02580572049520.130779938399-0.0530765012654-0.0042927855720.141959819619-0.0003610217693040.10398663773423.09552068376.483732400428.73041392625
31.840651320790.0243574942659-0.7588488938930.6378319994310.02393472138232.4982477150.0285001598277-0.0789352488321-0.0900094534273-0.02423937214530.02435027952360.0695061407466-0.0490501504328-0.204144791529-0.04959704472720.102761926807-0.000142971521114-0.03173734725870.1136907677940.02230641747990.1219399611418.84165439213-1.9639981039118.6755851694
42.62060257230.4967898769090.8088272881177.032738753572.687075210116.352361616650.205003491599-0.870347614974-0.06694950272890.452317606528-0.2761978918390.7612734754870.233309925825-1.210804077490.116317654720.167281654545-0.04388475458040.009465338645310.4997311752080.04659182357410.245441853913-3.32291795727-5.5073822523335.5691759791
51.227048306570.620320925402-2.418668270491.07868797575-1.446490947097.36343830637-0.0366234884993-0.0876574397938-0.06764264011750.07474921347790.0440301618611-0.07851469827420.00381487276180.0704161313192-0.01356631736490.1005532266820.0161198553886-0.03452780333840.1584964742750.02152149029840.1620612739257.84424120762-4.6218240449230.0438622865
67.74250526595-2.21366424152-0.1186847047912.49435868191-1.443406500674.30818361789-0.03252249188460.1401334478210.405663625810.0664560511510.002964081727470.0200051280428-0.256648430799-0.9773931821760.05453594048010.126584171277-0.0184304662525-0.02707343015550.2982709391980.06672723571320.1614334897351.997116768740.70139182453215.8568000785
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 19 through 31 )19 - 311 - 13
22chain 'A' and (resid 32 through 85 )32 - 8514 - 59
33chain 'A' and (resid 86 through 143 )86 - 14360 - 117
44chain 'A' and (resid 144 through 156 )144 - 156118 - 130
55chain 'A' and (resid 157 through 187 )157 - 187131 - 161
66chain 'A' and (resid 188 through 205 )188 - 205162 - 179

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