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- PDB-1o4w: CRYSTAL STRUCTURE OF a PIN (PILT N-TERMINUS) DOMAIN CONTAINING PR... -

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Entry
Database: PDB / ID: 1o4w
TitleCRYSTAL STRUCTURE OF a PIN (PILT N-TERMINUS) DOMAIN CONTAINING PROTEIN (AF0591) FROM ARCHAEOGLOBUS FULGIDUS AT 1.90 A RESOLUTION
ComponentsPIN (PilT N-terminus) domain
KeywordsTRANSLATION / PIN (PILT N-TERMINUS) DOMAIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
VapC9 PIN-like domain / PIN like domain / VapC family / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 A resolution
Authors: Levin, I. / Schwarzenbacher, R. / Page, R. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Campbell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / ...Authors: Levin, I. / Schwarzenbacher, R. / Page, R. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Campbell, J. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Quijano, K. / Reyes, R. / Rezezadeh, F. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJul 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE BIOLOGICAL UNIT IS PROPOSED TO BE A DIMER AROUND THE CRYTALLOGRAPHIC 2-FOLD AXIS. DIMERISATION IS MEDIATED BY AN EXPOSED 2-STRAND BETA SHEET COMPRISING THE HYDROPHILIC C-TERMINAL RESIDUES OF EACH SUBUNIT, THAT BRIDGES THE GLOBULAR DOMAINS OF EACH SUBUNIT. THIS IS CONSIDERED BIOLOGICALLY SIGNIFICANT BECAUSE OF IT LEADS TO CHAIN SWAPPING BETWEEN SUBUNITS.
Remark 650HELIX DETERMINATION METHOD: AUTHOR
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PIN (PilT N-terminus) domain


Theoretical massNumber of molelcules
Total (without water)17,1421
Polymers17,1421
Non-polymers00
Water1,62190
1
A: PIN (PilT N-terminus) domain

A: PIN (PilT N-terminus) domain


Theoretical massNumber of molelcules
Total (without water)34,2842
Polymers34,2842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
Buried area2330 Å2
ΔGint-17 kcal/mol
Surface area14090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.705, 63.705, 78.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE BIOLOGICAL UNIT IS PROPOSED TO BE A DIMER AROUND THE CRYTALLOGRAPHIC 2-FOLD AXIS. DIMERISATION IS MEDIATED BY AN EXPOSED 2-STRAND BETA SHEET COMPRISING THE HYDROPHILIC C-TERMINAL RESIDUES OF EACH SUBUNIT, THAT BRIDGES THE GLOBULAR DOMAINS OF EACH SUBUNIT. THIS IS CONSIDERED BIOLOGICALLY SIGNIFICANT BECAUSE OF IT LEADS TO CHAIN SWAPPING BETWEEN SUBUNITS. GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. APPLY THE FOLLOWING TO CHAINS: A, W BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 BIOMT2 2 0.000000 -1.000000 0.000000 110.69801 BIOMT3 2 0.000000 0.000000 -1.000000 -26.13300

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Components

#1: Protein PIN (PilT N-terminus) domain


Mass: 17142.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0591 / Production host: Escherichia coli (E. coli) / References: UniProt: O29664
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.04 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 30% MPD, MES buffer pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal grow
*PLUS
Details: Santarsiero, B.D., (2002) J. Appl. Crystallogr., 35, 278.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98397, 0.97922, 0.91837, 0.97855
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2003 / Details: flat mirror
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.983971
20.979221
30.918371
40.978551
ReflectionResolution: 1.9→31.86 Å / Num. all: 14860 / Num. obs: 14860 / % possible obs: 99.9 % / Redundancy: 8.8 % / Biso Wilson estimate: 48.07 Å2 / Rsym value: 0.05 / Net I/σ(I): 25.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1058 / Rsym value: 0.638 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14887 / Num. measured all: 131380 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.638

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→31.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.521 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The 9-sigma difference density peak on the crystallographic 2-fold axis between residues 126 and 128 was left unmodeled, but could indicate a metal ion. 2. The 2 TLS groups correspond to ...Details: 1. The 9-sigma difference density peak on the crystallographic 2-fold axis between residues 126 and 128 was left unmodeled, but could indicate a metal ion. 2. The 2 TLS groups correspond to globular and tail portions of protein respectively. 3. Hydrogens have been added in the riding positions.
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 728 4.9 %RANDOM
Rwork0.18843 ---
obs0.19059 14131 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.843 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20.52 Å20 Å2
2--1.05 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 0 90 1064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022998
X-RAY DIFFRACTIONr_bond_other_d0.0010.02965
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9841345
X-RAY DIFFRACTIONr_angle_other_deg0.75832223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0885124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2323.48843
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3915187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.595158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021090
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02206
X-RAY DIFFRACTIONr_nbd_refined0.2070.2176
X-RAY DIFFRACTIONr_nbd_other0.1580.2900
X-RAY DIFFRACTIONr_nbtor_other0.0810.2605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.27
X-RAY DIFFRACTIONr_mcbond_it0.7681.5621
X-RAY DIFFRACTIONr_mcangle_it1.4542998
X-RAY DIFFRACTIONr_scbond_it2.7973377
X-RAY DIFFRACTIONr_scangle_it4.3914.5347
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 63 5.92 %
Rwork0.284 1002 -
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)
14.59742.1167-0.64874.297-0.26293.52070.0334-0.22240.07340.1117-0.08490.0989-0.2143-0.09420.0515-0.067-0.08250.0478-0.2584-0.0177-0.176556.313247.72259.287
20.36660.3073-3.63670.6474-0.935847.52340.26360.0196-0.26990.2281-0.5630.1617-0.28941.50290.29930.05450.0914-0.02450.07530.0303-0.038860.096254.772-16.8151
Refinement TLS group

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

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1110 - 12222 - 134
22123 - 134135 - 146
Refinement
*PLUS
Num. reflection obs: 14859
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.23

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