PDB Short entry for 1K09 HEADER DE NOVO PROTEIN 18-SEP-01 1K09 TITLE SOLUTION STRUCTURE OF BETACORE, A DESIGNED WATER SOLUBLE FOUR-STRANDED TITLE 2 ANTIPARALLEL B-SHEET PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORE MODULE I; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CORE MODULE II; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 4 ORGANISM_COMMON: BOVINE; SOURCE 5 ORGANISM_TAXID: 9913; SOURCE 6 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID-PHASE SOURCE 7 PEPTIDE CHEMISTRY. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SOURCE 8 BOS TAURUS (BOVINE).; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 12 ORGANISM_COMMON: BOVINE; SOURCE 13 ORGANISM_TAXID: 9913; SOURCE 14 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED BY SOLID-PHASE SOURCE 15 PEPTIDE CHEMISTRY. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN SOURCE 16 BOS TAURUS (BOVINE). KEYWDS FOUR-STRANDED ANTIPARALLEL BETA-SHEET, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.CARULLA,C.WOODWARD,G.BARANY REVDAT 6 21-FEB-24 1K09 1 COMPND SOURCE REMARK DBREF REVDAT 6 2 1 SEQADV SEQRES HET HETNAM REVDAT 6 3 1 FORMUL LINK ATOM REVDAT 5 15-NOV-23 1K09 1 ATOM REVDAT 4 23-FEB-22 1K09 1 REMARK LINK REVDAT 3 24-FEB-09 1K09 1 VERSN REVDAT 2 01-APR-03 1K09 1 JRNL REVDAT 1 10-JUL-02 1K09 0 JRNL AUTH N.CARULLA,C.WOODWARD,G.BARANY JRNL TITL BETACORE, A DESIGNED WATER SOLUBLE FOUR-STRANDED JRNL TITL 2 ANTIPARALLEL BETA-SHEET PROTEIN. JRNL REF PROTEIN SCI. V. 11 1539 2002 JRNL REFN ISSN 0961-8368 JRNL PMID 12021452 JRNL DOI 10.1110/PS.4440102 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 195 RESTRAINTS, 172 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 14 DIHEDRAL ANGLE RESTRAINTS, 9 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS REMARK 4 REMARK 4 1K09 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014397. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 288 REMARK 210 PH : 3; 3 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.4 MM BETACORE SELECTIVELY-15N; REMARK 210 PH3; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N-HSQC-NOESY; REMARK 210 3D_15N-HSQC-TOCSY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMERS ARE REMARK 210 THOSE WITH NO CONSTRAINT REMARK 210 VIOLATIONS GREATER THAN 0.5 REMARK 210 ANGSTROMS FOR NOES AND 5 DEGREES REMARK 210 FOR DIHEDRALS. THEY ARE ALSO THE REMARK 210 ONES WITH BEST COVALENT GEOMETRY. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 8 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O ALA A 12 H LEU A 16 1.51 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 1 LYS A 2 93.96 62.95 REMARK 500 1 LYS A 4 105.32 -174.70 REMARK 500 1 ILE A 5 -165.00 -54.90 REMARK 500 1 ARG A 7 88.52 -154.67 REMARK 500 1 TYR A 10 170.59 48.22 REMARK 500 1 ASN A 11 67.24 162.35 REMARK 500 1 ALA A 12 -103.47 -44.13 REMARK 500 1 LYS A 13 84.84 45.74 REMARK 500 1 ABA A 17 90.28 175.55 REMARK 500 1 GLN A 18 102.65 -43.80 REMARK 500 1 LYS B 2 47.39 -83.41 REMARK 500 1 ALA B 3 -161.25 -108.68 REMARK 500 1 ARG B 4 64.69 63.76 REMARK 500 1 ARG B 7 91.92 -56.05 REMARK 500 1 PHE B 9 67.89 -150.22 REMARK 500 1 TYR B 10 102.60 -42.56 REMARK 500 1 LYS B 16 73.15 176.88 REMARK 500 1 ABA B 17 -162.09 39.14 REMARK 500 1 GLN B 18 155.27 169.61 REMARK 500 1 THR B 19 117.25 -162.53 REMARK 500 1 TYR B 22 24.40 -165.42 REMARK 500 2 ALA A 3 -120.68 -110.33 REMARK 500 2 LYS A 4 104.37 51.55 REMARK 500 2 ARG A 7 103.92 173.68 REMARK 500 2 LYS A 13 -82.07 -47.95 REMARK 500 2 VAL A 21 -79.31 -98.01 REMARK 500 2 TYR A 22 116.75 69.56 REMARK 500 2 ILE B 6 140.72 -170.46 REMARK 500 2 ARG B 7 147.71 -172.23 REMARK 500 2 TYR B 10 -86.36 -114.76 REMARK 500 2 ASN B 11 -34.08 175.28 REMARK 500 2 LYS B 13 -78.05 -41.88 REMARK 500 2 LYS B 16 140.10 64.67 REMARK 500 2 GLN B 18 87.83 -25.59 REMARK 500 2 VAL B 21 -148.85 -106.79 REMARK 500 2 TYR B 22 -165.79 40.25 REMARK 500 3 LYS A 2 -119.39 -128.76 REMARK 500 3 LYS A 4 103.82 -37.05 REMARK 500 3 ALA A 12 -116.93 -58.22 REMARK 500 3 LYS A 13 80.52 51.53 REMARK 500 3 LEU A 16 53.96 -150.25 REMARK 500 3 ABA A 17 108.15 -42.55 REMARK 500 3 ALA B 3 61.97 -110.89 REMARK 500 3 ARG B 4 -135.79 -131.09 REMARK 500 3 TYR B 10 107.51 -50.46 REMARK 500 3 LYS B 16 125.89 -38.31 REMARK 500 3 TYR B 22 51.29 -178.85 REMARK 500 4 ALA A 3 55.83 -105.68 REMARK 500 4 LYS A 13 -80.33 -49.77 REMARK 500 4 ALA B 3 -166.86 -110.34 REMARK 500 REMARK 500 THIS ENTRY HAS 274 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 7 0.27 SIDE CHAIN REMARK 500 1 ARG B 4 0.32 SIDE CHAIN REMARK 500 1 ARG B 7 0.17 SIDE CHAIN REMARK 500 2 ARG A 7 0.22 SIDE CHAIN REMARK 500 2 ARG B 4 0.15 SIDE CHAIN REMARK 500 2 ARG B 7 0.31 SIDE CHAIN REMARK 500 3 ARG A 7 0.14 SIDE CHAIN REMARK 500 3 ARG B 4 0.08 SIDE CHAIN REMARK 500 3 ARG B 7 0.18 SIDE CHAIN REMARK 500 4 ARG A 7 0.32 SIDE CHAIN REMARK 500 4 ARG B 4 0.21 SIDE CHAIN REMARK 500 4 ARG B 7 0.19 SIDE CHAIN REMARK 500 5 ARG A 7 0.30 SIDE CHAIN REMARK 500 5 ARG B 4 0.29 SIDE CHAIN REMARK 500 5 ARG B 7 0.22 SIDE CHAIN REMARK 500 6 ARG A 7 0.26 SIDE CHAIN REMARK 500 6 ARG B 4 0.29 SIDE CHAIN REMARK 500 6 ARG B 7 0.25 SIDE CHAIN REMARK 500 7 ARG A 7 0.30 SIDE CHAIN REMARK 500 7 ARG B 4 0.31 SIDE CHAIN REMARK 500 7 ARG B 7 0.20 SIDE CHAIN REMARK 500 8 ARG A 7 0.24 SIDE CHAIN REMARK 500 8 ARG B 4 0.13 SIDE CHAIN REMARK 500 8 ARG B 7 0.23 SIDE CHAIN REMARK 500 9 ARG A 7 0.32 SIDE CHAIN REMARK 500 9 ARG B 4 0.30 SIDE CHAIN REMARK 500 9 ARG B 7 0.23 SIDE CHAIN REMARK 500 10 ARG A 7 0.11 SIDE CHAIN REMARK 500 10 ARG B 4 0.31 SIDE CHAIN REMARK 500 10 ARG B 7 0.32 SIDE CHAIN REMARK 500 11 ARG A 7 0.29 SIDE CHAIN REMARK 500 11 ARG B 4 0.30 SIDE CHAIN REMARK 500 11 ARG B 7 0.27 SIDE CHAIN REMARK 500 12 ARG A 7 0.30 SIDE CHAIN REMARK 500 12 ARG B 4 0.26 SIDE CHAIN REMARK 500 12 ARG B 7 0.31 SIDE CHAIN REMARK 500 13 ARG A 7 0.11 SIDE CHAIN REMARK 500 13 ARG B 4 0.15 SIDE CHAIN REMARK 500 13 ARG B 7 0.32 SIDE CHAIN REMARK 500 14 ARG A 7 0.23 SIDE CHAIN REMARK 500 14 ARG B 4 0.25 SIDE CHAIN REMARK 500 14 ARG B 7 0.29 SIDE CHAIN REMARK 500 15 ARG A 7 0.09 SIDE CHAIN REMARK 500 15 ARG B 4 0.25 SIDE CHAIN REMARK 500 15 ARG B 7 0.17 SIDE CHAIN REMARK 500 16 ARG A 7 0.10 SIDE CHAIN REMARK 500 16 ARG B 4 0.20 SIDE CHAIN REMARK 500 16 ARG B 7 0.26 SIDE CHAIN REMARK 500 17 ARG A 7 0.26 SIDE CHAIN REMARK 500 17 ARG B 4 0.15 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 26 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 26 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THESE SYNTHETIC PEPTIDE (MINUS THE REMARK 999 MODIFIED AMINO ACIDS AND RESIDUE ASP 14) IS NATURALLY REMARK 999 FOUND IN BOVINE PANCREATIC TRYPSIN INHIBITOR. DBREF 1K09 A 1 25 UNP P00974 BPT1_BOVIN 49 73 DBREF 1K09 B 1 25 UNP P00974 BPT1_BOVIN 49 73 SEQADV 1K09 MPT A 1 UNP P00974 CYS 49 ENGINEERED MUTATION SEQADV 1K09 LYS A 4 UNP P00974 ARG 52 ENGINEERED MUTATION SEQADV 1K09 ASP A 14 UNP P00974 ALA 62 ENGINEERED MUTATION SEQADV 1K09 ABA A 17 UNP P00974 CYS 65 ENGINEERED MUTATION SEQADV 1K09 NH2 A 26 UNP P00974 AMIDATION SEQADV 1K09 MPT B 1 UNP P00974 CYS 49 ENGINEERED MUTATION SEQADV 1K09 ASP B 14 UNP P00974 ALA 62 ENGINEERED MUTATION SEQADV 1K09 LYS B 16 UNP P00974 LEU 64 ENGINEERED MUTATION SEQADV 1K09 ABA B 17 UNP P00974 CYS 65 ENGINEERED MUTATION SEQADV 1K09 NH2 B 26 UNP P00974 AMIDATION SEQRES 1 A 26 MPT LYS ALA LYS ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 2 A 26 ASP GLY LEU ABA GLN THR PHE VAL TYR GLY GLY CYS NH2 SEQRES 1 B 26 MPT LYS ALA ARG ILE ILE ARG TYR PHE TYR ASN ALA LYS SEQRES 2 B 26 ASP GLY LYS ABA GLN THR PHE VAL TYR GLY GLY CYS NH2 MODRES 1K09 ABA A 17 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1K09 ABA B 17 ALA ALPHA-AMINOBUTYRIC ACID HET MPT A 1 9 HET ABA A 17 13 HET NH2 A 26 3 HET MPT B 1 9 HET ABA B 17 13 HET NH2 B 26 3 HET C55 A 27 25 HETNAM MPT BETA-MERCAPTOPROPIONIC ACID HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM NH2 AMINO GROUP HETNAM C55 (7E)-4,9-DIOXO-6-OXA-3,7,10-TRIAZADODEC-7-ENE-1,12- HETNAM 2 C55 DIOIC ACID FORMUL 1 MPT 2(C3 H6 O2 S) FORMUL 1 ABA 2(C4 H9 N O2) FORMUL 1 NH2 2(H2 N) FORMUL 3 C55 C8 H11 N3 O7 LINK C MPT A 1 N LYS A 2 1555 1555 1.31 LINK SG MPT A 1 SG CYS A 25 1555 1555 2.02 LINK NZ LYS A 4 CH C55 A 27 1555 1555 1.31 LINK C LEU A 16 N ABA A 17 1555 1555 1.31 LINK C ABA A 17 N GLN A 18 1555 1555 1.31 LINK C CYS A 25 N NH2 A 26 1555 1555 1.31 LINK C1 C55 A 27 NZ LYS B 16 1555 1555 1.30 LINK C MPT B 1 N LYS B 2 1555 1555 1.31 LINK SG MPT B 1 SG CYS B 25 1555 1555 2.02 LINK C LYS B 16 N ABA B 17 1555 1555 1.31 LINK C ABA B 17 N GLN B 18 1555 1555 1.31 LINK C CYS B 25 N NH2 B 26 1555 1555 1.31 SITE 1 AC1 2 GLY A 24 CYS A 25 SITE 1 AC2 1 CYS B 25 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