HEADER DE NOVO PROTEIN 01-MAR-07 2P0X TITLE SOLUTION STRUCTURE OF A NON-BIOLOGICAL ATP-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABIOTIC ATP-BINDING, FOLDING OPTIMIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC GENE; SOURCE 3 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 4 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PIADL14; SOURCE 8 OTHER_DETAILS: SYNTHETIC GENE, ABIOTIC PROTEIN SELECTED BY MRNA- SOURCE 9 DISPLAY KEYWDS ALPHA/BETA FOLD; TREBLE CLEF ZINC BINDING MOTIF, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.S.MANSY,J.W.SZOSTAK,J.C.CHAPUT REVDAT 4 01-MAY-24 2P0X 1 REMARK REVDAT 3 24-FEB-09 2P0X 1 VERSN REVDAT 2 16-OCT-07 2P0X 1 REMARK REVDAT 1 07-AUG-07 2P0X 0 JRNL AUTH S.S.MANSY,J.ZHANG,R.KUMMERLE,M.NILSSON,J.J.CHOU,J.W.SZOSTAK, JRNL AUTH 2 J.C.CHAPUT JRNL TITL STRUCTURE AND EVOLUTIONARY ANALYSIS OF A NON-BIOLOGICAL JRNL TITL 2 ATP-BINDING PROTEIN JRNL REF J.MOL.BIOL. V. 371 501 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17583732 JRNL DOI 10.1016/J.JMB.2007.05.062 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.13, X-PLOR NIH 2.13 REMARK 3 AUTHORS : BRUNGER A. T. ET AL (X-PLOR), BRUNGER A. T. ET AL REMARK 3 (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 673 DISTANCE RESTRAINTS, 60 DIHEDRAL REMARK 3 ANGLE RESTRAINTS REMARK 4 REMARK 4 2P0X COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041828. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.064 M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM FOLDING OPTIMIZED PROTEIN REMARK 210 U-15N,13C; 10 MM SODIUM REMARK 210 PHOSPHATE, 50 MM KCL, 0.5 MM ATP, REMARK 210 PH 6.5; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA-J; 3D_15N-SEPARATED_NOESY; REMARK 210 HNHA; TROSY-HNCO; (H)CCH-TOCSY; REMARK 210 HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2006, BRUKER TOPSPIN 1.3 REMARK 210 METHOD USED : HYBRID DISTANCE GEOMETRY - REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-20 REMARK 470 RES CSSEQI ATOMS REMARK 470 THR A 64 O 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 GLY A 42 H ASP A 44 1.30 REMARK 500 O LYS A 32 HD21 ASN A 36 1.44 REMARK 500 O SER A 38 H ASP A 43 1.47 REMARK 500 O CYS A 34 H SER A 38 1.53 REMARK 500 H LYS A 21 O HIS A 24 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 19 C ARG A 19 O -0.135 REMARK 500 1 ARG A 26 C ARG A 26 O -0.131 REMARK 500 3 ARG A 19 C ARG A 19 O -0.159 REMARK 500 3 HIS A 24 C HIS A 24 O -0.151 REMARK 500 3 TRP A 52 C LEU A 53 N -0.180 REMARK 500 4 VAL A 50 C ASP A 51 N -0.138 REMARK 500 4 TRP A 52 C LEU A 53 N -0.173 REMARK 500 5 ARG A 19 C ARG A 19 O -0.139 REMARK 500 5 ARG A 26 C ARG A 26 O -0.148 REMARK 500 6 TRP A 52 C LEU A 53 N -0.174 REMARK 500 9 ARG A 19 C VAL A 20 N -0.197 REMARK 500 9 LEU A 25 C ARG A 26 N -0.169 REMARK 500 10 THR A 56 C ASP A 57 N -0.190 REMARK 500 11 TRP A 52 C LEU A 53 N -0.167 REMARK 500 12 TRP A 52 C LEU A 53 N -0.161 REMARK 500 13 ARG A 26 C ILE A 27 N -0.148 REMARK 500 13 TRP A 52 C LEU A 53 N -0.144 REMARK 500 15 ARG A 19 C VAL A 20 N -0.244 REMARK 500 16 TRP A 52 C LEU A 53 N -0.180 REMARK 500 17 TRP A 18 C ARG A 19 N -0.142 REMARK 500 17 ARG A 19 C VAL A 20 N -0.174 REMARK 500 17 VAL A 50 C ASP A 51 N -0.188 REMARK 500 18 TRP A 52 C LEU A 53 N -0.181 REMARK 500 19 TRP A 52 C LEU A 53 N -0.146 REMARK 500 20 ARG A 19 C ARG A 19 O -0.122 REMARK 500 20 ARG A 26 C ARG A 26 O -0.136 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 9 ARG A 26 O - C - N ANGL. DEV. = -12.2 DEGREES REMARK 500 10 TRP A 52 O - C - N ANGL. DEV. = -10.2 DEGREES REMARK 500 10 TYR A 55 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 15 TRP A 18 O - C - N ANGL. DEV. = -13.8 DEGREES REMARK 500 15 ARG A 19 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 17 TRP A 18 CA - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 17 TRP A 18 O - C - N ANGL. DEV. = -15.2 DEGREES REMARK 500 17 ARG A 19 O - C - N ANGL. DEV. = -13.9 DEGREES REMARK 500 17 HIS A 49 CA - C - N ANGL. DEV. = 13.9 DEGREES REMARK 500 17 HIS A 49 O - C - N ANGL. DEV. = -14.9 DEGREES REMARK 500 17 VAL A 50 O - C - N ANGL. DEV. = -13.6 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 1 PHE A 3 -128.01 -130.69 REMARK 500 1 LYS A 12 3.67 51.06 REMARK 500 1 ARG A 16 112.55 160.15 REMARK 500 1 ASP A 17 151.02 -33.98 REMARK 500 1 ASN A 22 92.09 27.45 REMARK 500 1 ARG A 23 -13.89 67.36 REMARK 500 1 CYS A 31 171.16 -56.96 REMARK 500 1 ASP A 43 -51.76 60.20 REMARK 500 1 ASP A 44 58.01 -157.98 REMARK 500 1 TYR A 46 2.58 52.00 REMARK 500 1 MET A 54 34.57 -71.15 REMARK 500 1 TYR A 55 -39.16 -169.89 REMARK 500 1 PHE A 61 -110.77 -94.89 REMARK 500 1 SER A 62 102.53 -48.18 REMARK 500 2 VAL A 5 92.82 -35.45 REMARK 500 2 CYS A 8 168.56 -46.65 REMARK 500 2 LYS A 12 10.82 42.22 REMARK 500 2 PRO A 15 -81.44 -72.23 REMARK 500 2 ARG A 16 108.25 172.86 REMARK 500 2 ASP A 17 131.31 -32.17 REMARK 500 2 ASN A 22 -114.95 39.15 REMARK 500 2 THR A 33 -70.78 -66.71 REMARK 500 2 ASP A 43 -62.94 59.02 REMARK 500 2 ASP A 44 58.06 -162.07 REMARK 500 2 THR A 45 42.31 -168.03 REMARK 500 2 LEU A 53 77.32 -109.54 REMARK 500 2 MET A 54 25.74 28.21 REMARK 500 2 TYR A 55 -37.63 174.48 REMARK 500 3 VAL A 5 -92.66 -128.11 REMARK 500 3 CYS A 8 169.71 -47.77 REMARK 500 3 VAL A 9 -24.87 -143.43 REMARK 500 3 CYS A 11 -33.96 -131.90 REMARK 500 3 LYS A 12 1.60 52.97 REMARK 500 3 PRO A 15 -73.58 -72.03 REMARK 500 3 ARG A 16 110.78 171.86 REMARK 500 3 ASP A 17 143.21 -37.36 REMARK 500 3 ASN A 22 88.14 22.55 REMARK 500 3 ARG A 23 -4.71 57.97 REMARK 500 3 LYS A 40 -70.50 -78.39 REMARK 500 3 ASP A 43 -65.22 56.49 REMARK 500 3 ASP A 44 57.14 -161.15 REMARK 500 3 THR A 45 -60.45 -155.52 REMARK 500 3 TYR A 46 43.84 -68.80 REMARK 500 3 MET A 54 2.74 -67.31 REMARK 500 3 TYR A 55 7.60 -174.16 REMARK 500 3 SER A 62 -63.66 -149.96 REMARK 500 3 SER A 63 100.75 48.63 REMARK 500 4 PHE A 3 -110.72 -102.34 REMARK 500 4 CYS A 8 175.31 -49.09 REMARK 500 4 CYS A 11 -31.44 -133.60 REMARK 500 REMARK 500 THIS ENTRY HAS 354 RAMACHANDRAN OUTLIERS. 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 A1319 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 CYS A 11 SG 104.4 REMARK 620 3 CYS A 31 SG 102.0 142.3 REMARK 620 4 CYS A 34 SG 108.8 106.6 89.4 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 1319 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1318 DBREF 2P0X A 1 64 PDB 2P0X 2P0X 1 64 SEQRES 1 A 64 GLY SER PHE ARG VAL LYS PRO CYS VAL VAL CYS LYS VAL SEQRES 2 A 64 ALA PRO ARG ASP TRP ARG VAL LYS ASN ARG HIS LEU ARG SEQRES 3 A 64 ILE TYR ASN MET CYS LYS THR CYS PHE ASN ASN SER ILE SEQRES 4 A 64 LYS SER GLY ASP ASP THR TYR HIS GLY HIS VAL ASP TRP SEQRES 5 A 64 LEU MET TYR THR ASP ALA LYS GLU PHE SER SER THR HET ZN A1319 1 HET ATP A1318 43 HETNAM ZN ZINC ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 ZN ZN 2+ FORMUL 3 ATP C10 H16 N5 O13 P3 HELIX 1 1 CYS A 31 SER A 41 1 11 SHEET 1 A 4 TRP A 18 LYS A 21 0 SHEET 2 A 4 HIS A 24 TYR A 28 -1 O ARG A 26 N ARG A 19 SHEET 3 A 4 HIS A 49 TRP A 52 -1 O VAL A 50 N ILE A 27 SHEET 4 A 4 ASP A 57 GLU A 60 -1 O ALA A 58 N ASP A 51 LINK SG CYS A 8 ZN ZN A1319 1555 1555 2.43 LINK SG CYS A 11 ZN ZN A1319 1555 1555 2.29 LINK SG CYS A 31 ZN ZN A1319 1555 1555 2.63 LINK SG CYS A 34 ZN ZN A1319 1555 1555 2.50 SITE 1 AC1 4 CYS A 8 CYS A 11 CYS A 31 CYS A 34 SITE 1 AC2 12 ASP A 17 ARG A 19 LYS A 21 ARG A 26 SITE 2 AC2 12 TYR A 28 ASN A 29 MET A 30 PHE A 35 SITE 3 AC2 12 TYR A 46 HIS A 47 GLY A 48 HIS A 49 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