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- PDB-1ryq: Putative DNA-directed RNA polymerase, subunit e'' from Pyrococcus... -

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Basic information

Entry
Database: PDB / ID: 1ryq
TitlePutative DNA-directed RNA polymerase, subunit e'' from Pyrococcus Furiosus Pfu-263306-001
ComponentsDNA-directed RNA polymerase, subunit e''Polymerase
KeywordsTRANSFERASE / Structural genomics / RNA polymerase / Zinc / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
Rubrerythrin, domain 2 - #90 / Archaeal transcription elongation factor Spt4 / Archaeal transcription elongation factor Spt4 superfamily / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Spt4/RpoE2 zinc finger / Rubrerythrin, domain 2 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Transcription elongation factor Spt4
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.38 Å
AuthorsLiu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Arendall III, W.B. / Rose, J.P. / Brereton, P.S. / Izumi, M. / Jenney Jr., F.E. / Lee, H.S. ...Liu, Z.-J. / Chen, L. / Tempel, W. / Shah, A. / Arendall III, W.B. / Rose, J.P. / Brereton, P.S. / Izumi, M. / Jenney Jr., F.E. / Lee, H.S. / Poole II, F.L. / Shah, C. / Sugar, F.J. / Adams, M.W.W. / Richardson, D.C. / Richardson, J.S. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Parameter-space screening: a powerful tool for high-throughput crystal structure determination.
Authors: Liu, Z.J. / Lin, D. / Tempel, W. / Praissman, J.L. / Rose, J.P. / Wang, B.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The high-throughput protein-to-structure pipeline at SECSG
Authors: Liu, Z.-J. / Tempel, W. / Ng, J.D. / Lin, D. / Shah, A.K. / Chen, L. / Horanyi, P.S. / Habel, J.E. / Kataeva, I.A. / Xu, H. / Yang, H. / Chang, J.C. / Huang, L. / Chang, S.H. / Zhou, W. / ...Authors: Liu, Z.-J. / Tempel, W. / Ng, J.D. / Lin, D. / Shah, A.K. / Chen, L. / Horanyi, P.S. / Habel, J.E. / Kataeva, I.A. / Xu, H. / Yang, H. / Chang, J.C. / Huang, L. / Chang, S.H. / Zhou, W. / Lee, D. / Praissman, J.L. / Zhang, H. / Newton, M.G. / Rose, J.P. / Richardson, J.S. / Richardson, D.C. / Wang, B.C.
History
DepositionDec 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 6THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M. ...THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H.-S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) UNDER THE DIRECTION OF M.W.W.ADAMS.
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 999SEQUENCE Residue identifiers for the HIS tag coordinates are tentative. Discontinuous electron ...SEQUENCE Residue identifiers for the HIS tag coordinates are tentative. Discontinuous electron density at the N-terminus of the peptide does not permit a confident alignment of the visible histidine residues with the clone sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase, subunit e''
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9432
Polymers7,8781
Non-polymers651
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.534, 45.534, 50.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA-directed RNA polymerase, subunit e'' / Polymerase


Mass: 7877.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U440
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.93 Å3/Da / Density % sol: 36.21 %
Crystal growTemperature: 297 K / pH: 6.6
Details: 100mM sodium citrate, 25% PEG 3000, pH 6.6, modified batch crystallization, temperature 297K, pH 6.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 12502 / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.207 / % possible all: 79.9

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.5 Å / D res low: 20 Å / FOM : 0.45 / Reflection: 2269
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1I19.6790.6820.4750.140.88
2I27.4020.710.170.1330.226
3I9.760.7880.2210.0830.123
Phasing MAD shell
Resolution (Å)FOM Reflection
8.52-200.37130
5.54-8.520.41200
4.38-5.540.45240
3.74-4.380.45284
3.31-3.740.47316
3-3.310.49340
2.77-30.45359
2.58-2.770.46400
Phasing dmFOM : 0.54 / FOM acentric: 0.55 / FOM centric: 0.46 / Reflection: 3676 / Reflection acentric: 3015 / Reflection centric: 661
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
19.771-60.870.870.6418510877
6-3.80.820.880.68518384134
3.8-30.770.820.55638520118
3-2.60.650.70.43623520103
2.6-2.30.360.370.271094945149
2.3-2.10.190.180.2161853880

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.1.24 24/04/2001refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→39.53 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20435 607 4.9 %RANDOM
Rwork0.19321 ---
obs0.19374 11867 97.31 %-
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: 18.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.38→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms489 0 1 34 524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021499
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.913673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.508562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021
X-RAY DIFFRACTIONr_nbd_refined0.1840.2198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.9062314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0743507
X-RAY DIFFRACTIONr_scbond_it3.212185
X-RAY DIFFRACTIONr_scangle_it5.0663166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 40
Rwork0.219 746

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