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- PDB-4bxz: RNA Polymerase II-Bye1 complex -

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Basic information

Entry
Database: PDB / ID: 4bxz
TitleRNA Polymerase II-Bye1 complex
Components
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...) x 7
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...) x 5
  • TRANSCRIPTION FACTOR BYE1
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / : / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / positive regulation of translational initiation / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic ...Spen paralogue and orthologue SPOC, C-terminal / SPOC domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger, PHD-type, conserved site / PHD-finger / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Zinc finger PHD-type signature. / S1 domain / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / Transcription factor BYE1 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å
AuthorsKinkelin, K. / Wozniak, G.G. / Rothbart, S.B. / Lidschreiber, M. / Strahl, B.D. / Cramer, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of RNA Polymerase II Complexes with Bye1, a Chromatin-Binding Phf3/Dido1 Homologue
Authors: Kinkelin, K. / Wozniak, G.G. / Rothbart, S.B. / Lidschreiber, M. / Strahl, B.D. / Cramer, P.
History
DepositionJul 16, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Sep 6, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
B: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
C: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
X: TRANSCRIPTION FACTOR BYE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)582,71322
Polymers582,16513
Non-polymers5489
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.550, 392.090, 279.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 7 types, 7 molecules ABCDGIK

#1: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III ...RNA POLYMERASE II SUBUNIT 1 / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II SUBUNIT B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / RNA POLYMERASE II SUBUNIT 2 / B150 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT 3 / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P16370, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / RNA POLYMERASE II SUBUNIT B4 / B32 / DNA-DIRECTED RNA POLYMERASE II 32 KDA POLYPEPTIDE


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / RNA POLYMERASE II SUBUNIT B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA- ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P27999, DNA-directed RNA polymerase
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / RNA POLYMERASE II SUBUNIT B11 / B13.6 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P38902, DNA-directed RNA polymerase

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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20434, DNA-directed RNA polymerase
#6: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 23 KDA POLYPEPTIDE


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20435, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 14.5 KDA POLYPEPTIDE


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P20436, DNA-directed RNA polymerase
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 8.3 KDA POLYPEPTIDE


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P22139, DNA-directed RNA polymerase
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P40422, DNA-directed RNA polymerase

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Protein , 1 types, 1 molecules X

#13: Protein TRANSCRIPTION FACTOR BYE1 / BYPASS OF ESS1 PROTEIN 1


Mass: 68007.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P36106

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Non-polymers , 2 types, 9 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Sequence detailsCHAIN X IS BUILT AS POLY ALANINE, CORRESPONDING TO UNP P36106

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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: 5.2 Å3/Da / Density % sol: 76 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 750 MM TRI-SODIUM CITRATE, 100 MM HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91887
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2011
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR SI(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91887 Å / Relative weight: 1
ReflectionResolution: 4.8→49.63 Å / Num. obs: 59394 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 135.76 Å2 / Rmerge(I) obs: 0.41 / Net I/σ(I): 6.05
Reflection shellResolution: 4.8→4.92 Å / Redundancy: 7.82 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.24 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WCM

1wcm


Resolution: 4.8→49.63 Å / Cor.coef. Fo:Fc: 0.9236 / Cor.coef. Fo:Fc free: 0.8772 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.852
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31501. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN MG. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=31501. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=9.
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 1172 1.97 %RANDOM
Rwork0.1906 ---
obs0.1918 59394 99.97 %-
Displacement parametersBiso mean: 199 Å2
Baniso -1Baniso -2Baniso -3
1-5.8417 Å20 Å20 Å2
2--40.7146 Å20 Å2
3----46.5563 Å2
Refine analyzeLuzzati coordinate error obs: 1.197 Å
Refinement stepCycle: LAST / Resolution: 4.8→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31500 0 9 0 31509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0132054HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3343304HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d11447SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes849HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4603HARMONIC5
X-RAY DIFFRACTIONt_it32054HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion25.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4269SEMIHARMONIC5
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_contact38993SEMIHARMONIC4
LS refinement shellResolution: 4.8→4.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2754 89 2.05 %
Rwork0.2416 4258 -
all0.2423 4347 -
obs--99.97 %
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)
11.29290.237-0.04891.01940.11730.30580.124-0.01610.65710.184-0.14150.0056-0.09160.06420.0176-0.03110.09750.0158-0.29210.1129-0.2148115.31561.1462-6.0092
21.0171-0.4419-0.08932.0451-0.38110.3166-0.1488-0.13470.19670.50120.23470.8328-0.1664-0.1456-0.0859-0.0321-0.00230.2351-0.2881-0.0817-0.014982.03650.24918.707
32.46450.38691.0041.85220.49851.8823-0.132-0.6162-0.12750.8778-0.10970.1910.3449-0.04190.24170.56530.03560.1476-0.19990.0949-0.6043110.00615.945336.4865
44.6275-1.05884.697510.0525-4.62988.0347-0.01580.1999-0.57140.05850.39030.02-0.29340.6313-0.3745-0.23110.03590.04280.1492-0.2235-0.468136.35529.5498-65.4998
54.05192.2765-2.239814.1594-3.42032.8622-0.0367-0.20341.0434-0.44350.11950.0126-0.9930.311-0.0828-0.1608-0.11480.0072-0.27510.29050.1712127.15592.952-24.4906
68.95844.3036-1.00186.97910.21282.54380.0795-0.22330.77230.1297-0.2161-0.24520.60080.55660.13650.31750.15730.0259-0.1284-0.1247-0.4482139.42838.6839-19.0067
70.4316-0.54111.833700.25717.1534-0.274-0.1303-0.0269-0.08270.19660.091-0.0026-0.22650.07740.15430.18180.20950.2166-0.096-0.3032126.04823.7125-59.0481
814.58922.77944.18824.29760.77951.0333-0.0719-0.39210.07160.0284-0.0063-0.4836-0.66380.22040.07820.1079-0.207-0.304-0.0312-0.0074-0.2693152.18751.462537.495
92.9202-2.9155-0.07835.3157-0.94440.2755-0.0877-0.09250.19190.3011-0.1660.0655-0.03440.25410.2537-0.20440.24130.3025-0.4287-0.03320.49577.026899.392314.1501
102.9743-2.27363.91250.00511.47826.6941-0.0074-0.33180.1229-0.0391-0.00420.2549-0.0212-0.09330.01150.60780.04470.28150.11790.118-0.522790.736825.345637.8989
110.72814.2483-0.73238.09461.99881.22040.087-0.0196-0.4207-0.56320.2579-0.4047-0.63980.0067-0.34490.10150.1118-0.06230.083-0.22750.6014106.949124.9410.8655
123.4367-3.06491.57457.2661-3.89584.85340.06930.5868-0.22880.5583-0.2809-0.68090.33110.27280.21150.21750.1018-0.20020.04750.144-0.5421131.17216.920128.5743
132.7012.89073.38972.2421.39760.7269-0.0022-0.1704-0.0764-0.043-0.2250.51950.2478-0.11260.22720.03-0.16050.1587-0.18860.19160.196575.80649.88749.0963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN X
12X-RAY DIFFRACTION12CHAIN K
13X-RAY DIFFRACTION13CHAIN L

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