HEADER DNA BINDING PROTEIN 19-JUL-19 6PV0 TITLE BACKBONE-MODIFIED VARIANT OF ZINC FINGER 2 FROM THE TRANSCRIPTION TITLE 2 FACTOR SP1 DNA BINDING DOMAIN: D-PRO IN THE METAL-BINDING TURN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR SP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA-BINDING DOMAIN, ZINC FINGER 2 RESIDUES 654-684; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ZINC FINGER, PROTEOMIMETIC, FOLDAMER, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.R.RAO,W.S.HORNE REVDAT 4 15-NOV-23 6PV0 1 REMARK REVDAT 3 14-JUN-23 6PV0 1 REMARK REVDAT 2 31-MAR-21 6PV0 1 JRNL REVDAT 1 24-JUN-20 6PV0 0 JRNL AUTH S.R.RAO,W.S.HORNE JRNL TITL PROTEOMIMETIC ZINC FINGER DOMAINS WITH MODIFIED JRNL TITL 2 METAL-BINDING BETA-TURNS. JRNL REF PEPT SCI (HOBOKEN) V. 112 2020 JRNL REFN ISSN 2475-8817 JRNL PMID 33733039 JRNL DOI 10.1002/PEP2.24177 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6PV0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000243140. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.2 MM ZINC FINGER 2 FROM REMARK 210 TRANSCRIPTION FACTOR SP1 DNA- REMARK 210 BINDING DOMAIN, D-PRO TURN REMARK 210 VARIANT, 10 MM [U-2H] TRIS, 0.05 REMARK 210 MM DSS, 1.8 MM ZINC CHLORIDE, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 3 THR A 28 -56.92 74.87 REMARK 500 4 THR A 28 69.19 -104.03 REMARK 500 9 HIS A 27 -63.73 -90.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 5 SG REMARK 620 2 CYS A 10 SG 110.9 REMARK 620 3 HIS A 23 NE2 110.0 108.9 REMARK 620 4 HIS A 27 NE2 107.9 110.3 108.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VA2 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF NATIVE DOMAIN REMARK 900 RELATED ID: 1SP2 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF NATIVE DOMAIN REMARK 900 RELATED ID: 30641 RELATED DB: BMRB REMARK 900 BACKBONE-MODIFIED VARIANT OF ZINC FINGER 2 FROM THE TRANSCRIPTION REMARK 900 FACTOR SP1 DNA BINDING DOMAIN: D-PRO IN THE METAL-BINDING TURN DBREF 6PV0 A 1 31 UNP P08047 SP1_HUMAN 654 684 SEQADV 6PV0 NLE A 4 UNP P08047 MET 657 VARIANT SEQADV 6PV0 DPR A 8 UNP P08047 SER 661 VARIANT SEQADV 6PV0 GLY A 9 UNP P08047 TYR 662 VARIANT SEQADV 6PV0 NH2 A 32 UNP P08047 AMIDATION SEQRES 1 A 32 ARG PRO PHE NLE CYS THR TRP DPR GLY CYS GLY LYS ARG SEQRES 2 A 32 PHE THR ARG SER ASP GLU LEU GLN ARG HIS LYS ARG THR SEQRES 3 A 32 HIS THR GLY GLU LYS NH2 HET NLE A 4 19 HET DPR A 8 14 HET NH2 A 32 3 HET ZN A 101 1 HETNAM NLE NORLEUCINE HETNAM DPR D-PROLINE HETNAM NH2 AMINO GROUP HETNAM ZN ZINC ION FORMUL 1 NLE C6 H13 N O2 FORMUL 1 DPR C5 H9 N O2 FORMUL 1 NH2 H2 N FORMUL 2 ZN ZN 2+ HELIX 1 AA1 ARG A 16 THR A 28 1 13 SHEET 1 AA1 2 PHE A 3 NLE A 4 0 SHEET 2 AA1 2 ARG A 13 PHE A 14 -1 O PHE A 14 N PHE A 3 LINK C PHE A 3 N NLE A 4 1555 1555 1.32 LINK C NLE A 4 N CYS A 5 1555 1555 1.33 LINK C TRP A 7 N DPR A 8 1555 1555 1.34 LINK C DPR A 8 N GLY A 9 1555 1555 1.33 LINK C LYS A 31 N NH2 A 32 1555 1555 1.32 LINK SG CYS A 5 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.30 LINK NE2 HIS A 23 ZN ZN A 101 1555 1555 1.99 LINK NE2 HIS A 27 ZN ZN A 101 1555 1555 2.00 SITE 1 AC1 4 CYS A 5 CYS A 10 HIS A 23 HIS A 27 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1