HEADER DE NOVO PROTEIN 21-FEB-07 2JO5 TITLE TETRAMERIC STRUCTURE OF KIA7F PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: KIA7F; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS OLIGOMER, PREBIOTIC, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.LOPEZ DE LA OSA,C.GONZALEZ,D.V.LAURENTS,A.CHAKRABARTTY,D.A.BATEMAN REVDAT 5 20-DEC-23 2JO5 1 REMARK REVDAT 4 09-MAR-22 2JO5 1 REMARK LINK REVDAT 3 24-FEB-09 2JO5 1 VERSN REVDAT 2 23-SEP-08 2JO5 1 JRNL REVDAT 1 18-SEP-07 2JO5 0 JRNL AUTH J.LOPEZ DE LA OSA,D.A.BATEMAN,S.HO,C.GONZALEZ, JRNL AUTH 2 A.CHAKRABARTTY,D.V.LAURENTS JRNL TITL GETTING SPECIFICITY FROM SIMPLICITY IN PUTATIVE PROTEINS JRNL TITL 2 FROM THE PREBIOTIC EARTH. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 14941 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17855563 JRNL DOI 10.1073/PNAS.0706876104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, AMBER 7.0 REMARK 3 AUTHORS : GUNTERT, BRAUN AND WUTHRICH (DYANA), CASE, DARDEN, REMARK 3 CHEATHAM, III, SIMMERLING, WANG, DUKE, LUO, AND REMARK 3 KOLL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JO5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000100077. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM PROTEIN, 10 MM SODIUM REMARK 210 ACETATE, 200 MM SODIUM CHLORIDE, REMARK 210 0.005 MM DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 250 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 LYS B 32 CE LYS B 32 NZ -0.263 REMARK 500 1 LYS B 39 CD LYS B 39 CE -0.216 REMARK 500 2 LYS C 61 CE LYS C 61 NZ -0.269 REMARK 500 2 LYS D 69 CE LYS D 69 NZ -0.167 REMARK 500 3 LYS A 3 CG LYS A 3 CD -0.284 REMARK 500 3 LYS B 39 CD LYS B 39 CE -0.246 REMARK 500 4 LYS A 17 CE LYS A 17 NZ -0.367 REMARK 500 4 LYS B 39 CD LYS B 39 CE -0.214 REMARK 500 4 LYS B 39 CE LYS B 39 NZ -0.164 REMARK 500 4 LYS C 61 CD LYS C 61 CE -0.291 REMARK 500 4 LYS D 69 CE LYS D 69 NZ -0.367 REMARK 500 4 LYS D 76 CE LYS D 76 NZ -0.220 REMARK 500 5 LYS B 32 CD LYS B 32 CE -0.368 REMARK 500 5 LYS B 39 CE LYS B 39 NZ -0.155 REMARK 500 5 LYS C 47 CD LYS C 47 CE -0.407 REMARK 500 5 LYS D 69 CD LYS D 69 CE -0.552 REMARK 500 5 LYS D 69 CE LYS D 69 NZ -0.159 REMARK 500 6 LYS A 3 CD LYS A 3 CE -0.279 REMARK 500 6 LYS A 17 CE LYS A 17 NZ -0.361 REMARK 500 7 LYS A 17 CD LYS A 17 CE -0.151 REMARK 500 7 LYS C 47 CE LYS C 47 NZ -0.260 REMARK 500 7 LYS C 61 CE LYS C 61 NZ -0.442 REMARK 500 8 LYS A 10 CE LYS A 10 NZ -0.213 REMARK 500 8 LYS B 32 CD LYS B 32 CE -0.267 REMARK 500 8 LYS B 32 CE LYS B 32 NZ -0.423 REMARK 500 8 LYS C 61 CD LYS C 61 CE -0.304 REMARK 500 9 LYS A 3 CE LYS A 3 NZ -0.169 REMARK 500 10 LYS B 32 CE LYS B 32 NZ -0.534 REMARK 500 10 LYS B 39 CD LYS B 39 CE -0.188 REMARK 500 10 LYS C 47 CE LYS C 47 NZ -0.313 REMARK 500 10 LYS D 76 CE LYS D 76 NZ -0.278 REMARK 500 10 LYS D 83 CE LYS D 83 NZ -0.182 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 PHE B 43 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 2 PHE B 43 CB - CG - CD1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 LYS B 39 CD - CE - NZ ANGL. DEV. = 19.1 DEGREES REMARK 500 4 ILE C 56 CB - CG1 - CD1 ANGL. DEV. = 31.0 DEGREES REMARK 500 5 LYS B 32 CD - CE - NZ ANGL. DEV. = 24.0 DEGREES REMARK 500 5 LYS D 69 CD - CE - NZ ANGL. DEV. = 15.8 DEGREES REMARK 500 6 ILE A 12 CB - CG1 - CD1 ANGL. DEV. = 18.2 DEGREES REMARK 500 6 PHE A 21 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 6 PHE A 21 CB - CG - CD1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 LYS B 32 CD - CE - NZ ANGL. DEV. = 18.6 DEGREES 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 2 ALA A 8 -83.17 -71.69 REMARK 500 2 ILE C 56 -60.58 -108.60 REMARK 500 6 ALA B 26 -19.92 -45.75 REMARK 500 6 ALA D 77 -72.38 -65.33 REMARK 500 7 ILE B 34 -52.37 -121.54 REMARK 500 7 ALA D 77 -74.85 -60.31 REMARK 500 9 ALA A 11 -76.97 -64.39 REMARK 500 10 ALA B 33 -76.55 -60.34 REMARK 500 10 ALA C 52 -82.21 -74.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA B 27 ALA B 28 2 148.93 REMARK 500 ALA A 5 ALA A 6 3 146.94 REMARK 500 ALA D 71 ALA D 72 4 149.87 REMARK 500 ALA C 49 ALA C 50 5 148.79 REMARK 500 ALA D 71 ALA D 72 6 149.84 REMARK 500 LYS D 76 ALA D 77 6 149.05 REMARK 500 ALA A 5 ALA A 6 7 146.93 REMARK 500 ALA D 71 ALA D 72 7 148.85 REMARK 500 LYS A 10 ALA A 11 9 148.77 REMARK 500 ALA C 50 ALA C 51 9 149.75 REMARK 500 ALA D 71 ALA D 72 9 147.78 REMARK 500 LYS B 32 ALA B 33 10 145.64 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 PHE B 43 0.08 SIDE CHAIN REMARK 500 1 PHE C 65 0.08 SIDE CHAIN REMARK 500 2 PHE D 87 0.09 SIDE CHAIN REMARK 500 3 PHE C 65 0.09 SIDE CHAIN REMARK 500 3 PHE D 87 0.13 SIDE CHAIN REMARK 500 4 PHE A 21 0.12 SIDE CHAIN REMARK 500 4 PHE B 43 0.09 SIDE CHAIN REMARK 500 4 PHE D 87 0.09 SIDE CHAIN REMARK 500 6 PHE B 43 0.08 SIDE CHAIN REMARK 500 6 PHE C 65 0.10 SIDE CHAIN REMARK 500 6 PHE D 87 0.14 SIDE CHAIN REMARK 500 7 PHE A 21 0.09 SIDE CHAIN REMARK 500 7 PHE C 65 0.11 SIDE CHAIN REMARK 500 9 PHE A 21 0.13 SIDE CHAIN REMARK 500 9 PHE B 43 0.10 SIDE CHAIN REMARK 500 9 PHE D 87 0.08 SIDE CHAIN REMARK 500 10 PHE B 43 0.09 SIDE CHAIN REMARK 500 10 PHE C 65 0.08 SIDE CHAIN REMARK 500 10 PHE D 87 0.09 SIDE CHAIN 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 ACE A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 22 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE B 23 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 44 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE C 45 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 C 66 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE D 67 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 D 88 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JO4 RELATED DB: PDB DBREF 2JO5 A 1 22 PDB 2JO5 2JO5 1 22 DBREF 2JO5 B 23 44 PDB 2JO5 2JO5 23 44 DBREF 2JO5 C 45 66 PDB 2JO5 2JO5 45 66 DBREF 2JO5 D 67 88 PDB 2JO5 2JO5 67 88 SEQRES 1 A 22 ACE ALA LYS ALA ALA ALA ALA ALA ILE LYS ALA ILE ALA SEQRES 2 A 22 ALA ILE ILE LYS ALA GLY GLY PHE NH2 SEQRES 1 B 22 ACE ALA LYS ALA ALA ALA ALA ALA ILE LYS ALA ILE ALA SEQRES 2 B 22 ALA ILE ILE LYS ALA GLY GLY PHE NH2 SEQRES 1 C 22 ACE ALA LYS ALA ALA ALA ALA ALA ILE LYS ALA ILE ALA SEQRES 2 C 22 ALA ILE ILE LYS ALA GLY GLY PHE NH2 SEQRES 1 D 22 ACE ALA LYS ALA ALA ALA ALA ALA ILE LYS ALA ILE ALA SEQRES 2 D 22 ALA ILE ILE LYS ALA GLY GLY PHE NH2 HET ACE A 1 6 HET NH2 A 22 3 HET ACE B 23 6 HET NH2 B 44 3 HET ACE C 45 6 HET NH2 C 66 3 HET ACE D 67 6 HET NH2 D 88 3 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP FORMUL 1 ACE 4(C2 H4 O) FORMUL 1 NH2 4(H2 N) HELIX 1 1 ALA A 4 GLY A 20 1 17 HELIX 2 2 ALA B 28 GLY B 42 1 15 HELIX 3 3 ALA C 48 GLY C 64 1 17 HELIX 4 4 ALA D 70 GLY D 86 1 17 LINK C ACE A 1 N ALA A 2 1555 1555 1.31 LINK C PHE A 21 N NH2 A 22 1555 1555 1.32 LINK C ACE B 23 N ALA B 24 1555 1555 1.32 LINK C PHE B 43 N NH2 B 44 1555 1555 1.30 LINK C ACE C 45 N ALA C 46 1555 1555 1.32 LINK C PHE C 65 N NH2 C 66 1555 1555 1.29 LINK C ACE D 67 N ALA D 68 1555 1555 1.32 LINK C PHE D 87 N NH2 D 88 1555 1555 1.29 SITE 1 AC1 4 ALA A 2 LYS A 3 ALA A 4 GLY B 42 SITE 1 AC2 4 ILE A 16 GLY A 20 PHE A 21 LYS D 76 SITE 1 AC3 5 ALA A 18 GLY A 19 GLY A 20 PHE A 21 SITE 2 AC3 5 ALA B 24 SITE 1 AC4 4 ACE A 1 GLY B 42 PHE B 43 ILE C 53 SITE 1 AC5 4 ALA C 46 LYS C 47 ALA C 48 GLY D 86 SITE 1 AC6 5 ALA B 28 LYS B 32 ILE C 60 GLY C 64 SITE 2 AC6 5 PHE C 65 SITE 1 AC7 4 ILE C 59 GLY C 64 PHE C 65 ALA D 68 SITE 1 AC8 8 ALA A 5 ALA A 6 ILE A 9 ACE C 45 SITE 2 AC8 8 ALA C 46 ILE D 82 GLY D 86 PHE D 87 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 HETATM 1 C ACE A 1 3.291 12.600 -1.205 1.00 0.00 C HETATM 2 O ACE A 1 3.591 11.953 -2.192 1.00 0.00 O HETATM 3 CH3 ACE A 1 4.226 13.605 -0.583 1.00 0.00 C HETATM 4 H1 ACE A 1 4.646 13.610 -0.475 1.00 0.00 H HETATM 5 H2 ACE A 1 4.400 14.032 -0.681 1.00 0.00 H HETATM 6 H3 ACE A 1 4.282 13.856 -0.165 1.00 0.00 H