HEADER PROTEIN BINDING 14-MAR-03 1UAP TITLE NMR STRUCTURE OF THE NTR DOMAIN FROM HUMAN PCOLCE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROCOLLAGEN C-PROTEINASE ENHANCER PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NTR DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PCOLCE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BETA BARREL, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR E.LIEPINSH,L.BANYAI,G.PINTACUDA,M.TREXLER,L.PATTHY,G.OTTING REVDAT 4 27-DEC-23 1UAP 1 REMARK REVDAT 3 02-MAR-22 1UAP 1 REMARK SEQADV REVDAT 2 24-FEB-09 1UAP 1 VERSN REVDAT 1 15-JUL-03 1UAP 0 JRNL AUTH E.LIEPINSH,L.BANYAI,G.PINTACUDA,M.TREXLER,L.PATTHY,G.OTTING JRNL TITL NMR STRUCTURE OF THE NETRIN-LIKE DOMAIN (NTR) OF HUMAN TYPE JRNL TITL 2 I PROCOLLAGEN C-PROTEINASE ENHANCER DEFINES STRUCTURAL JRNL TITL 3 CONSENSUS OF NTR DOMAINS AND ASSESSES POTENTIAL PROTEINASE JRNL TITL 4 INHIBITORY ACTIVITY AND LIGAND BINDING. JRNL REF J.BIOL.CHEM. V. 278 25982 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 12670942 JRNL DOI 10.1074/JBC.M302734200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL 2.6 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UAP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000005624. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301; 301 REMARK 210 PH : 5.5; 7.5 REMARK 210 IONIC STRENGTH : 0.05; 0.05 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM NTR(PCOLCE1) U-15N; 1MM REMARK 210 NTR(PCOLCE1); 1MM NTR(PCOLCE1) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; 2D TOCSY; DQF-COSY; HNHB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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 35 NE - CZ - NH2 ANGL. DEV. = -3.5 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 PRO A 28 -167.15 -79.60 REMARK 500 1 THR A 29 160.28 -49.66 REMARK 500 1 LEU A 72 81.23 37.49 REMARK 500 1 TYR A 76 -41.32 -131.02 REMARK 500 1 THR A 78 59.65 -142.42 REMARK 500 1 PRO A 87 -157.10 -70.62 REMARK 500 1 THR A 88 133.63 -34.74 REMARK 500 1 ASN A 119 -32.52 -177.40 REMARK 500 1 SER A 151 85.42 -166.40 REMARK 500 2 PRO A 62 134.06 -38.59 REMARK 500 2 LEU A 72 77.90 38.11 REMARK 500 2 TYR A 76 -33.36 -135.31 REMARK 500 2 PRO A 87 -152.61 -78.14 REMARK 500 2 THR A 88 123.76 -33.17 REMARK 500 2 ASN A 119 -26.87 -177.34 REMARK 500 2 LEU A 124 76.11 -119.96 REMARK 500 3 ASP A 26 33.57 -74.64 REMARK 500 3 LEU A 72 83.16 36.07 REMARK 500 3 PRO A 87 -154.17 -76.18 REMARK 500 3 THR A 88 123.90 -33.06 REMARK 500 3 PRO A 103 86.95 -68.27 REMARK 500 3 ASN A 119 -40.36 -170.01 REMARK 500 3 LEU A 124 78.98 -114.89 REMARK 500 3 SER A 151 74.29 -157.49 REMARK 500 4 PRO A 62 171.45 -59.18 REMARK 500 4 LEU A 72 79.94 40.65 REMARK 500 4 PRO A 87 -153.98 -73.35 REMARK 500 4 THR A 88 125.19 -34.61 REMARK 500 4 ASN A 119 -35.87 -179.08 REMARK 500 4 LEU A 124 74.31 -115.41 REMARK 500 4 PRO A 153 -153.91 -88.32 REMARK 500 5 LEU A 72 80.87 39.06 REMARK 500 5 PRO A 87 -152.69 -73.98 REMARK 500 5 THR A 88 125.76 -33.80 REMARK 500 5 ASN A 119 -41.92 -162.68 REMARK 500 5 SER A 151 93.41 -166.27 REMARK 500 6 ASP A 26 33.24 -141.74 REMARK 500 6 LEU A 72 81.09 39.17 REMARK 500 6 TYR A 76 -25.18 -141.38 REMARK 500 6 PRO A 87 -153.46 -68.06 REMARK 500 6 THR A 88 134.44 -35.01 REMARK 500 6 ASN A 119 -39.29 -178.18 REMARK 500 6 GLU A 127 37.20 -83.96 REMARK 500 6 SER A 151 73.08 -165.56 REMARK 500 7 LEU A 72 82.38 37.02 REMARK 500 7 TYR A 76 -32.01 -141.42 REMARK 500 7 PRO A 87 -153.00 -78.18 REMARK 500 7 THR A 88 125.44 -33.36 REMARK 500 7 PRO A 103 95.56 -68.63 REMARK 500 7 ASN A 119 -24.94 165.44 REMARK 500 REMARK 500 THIS ENTRY HAS 153 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 PHE A 94 0.09 SIDE CHAIN REMARK 500 1 ARG A 147 0.14 SIDE CHAIN REMARK 500 2 PHE A 94 0.09 SIDE CHAIN REMARK 500 3 TYR A 95 0.09 SIDE CHAIN REMARK 500 3 ARG A 120 0.08 SIDE CHAIN REMARK 500 4 TYR A 110 0.07 SIDE CHAIN REMARK 500 5 TYR A 95 0.08 SIDE CHAIN REMARK 500 5 ARG A 147 0.10 SIDE CHAIN REMARK 500 7 TYR A 95 0.07 SIDE CHAIN REMARK 500 8 ARG A 60 0.10 SIDE CHAIN REMARK 500 10 ARG A 35 0.09 SIDE CHAIN REMARK 500 10 ARG A 120 0.08 SIDE CHAIN REMARK 500 13 TYR A 76 0.13 SIDE CHAIN REMARK 500 14 ARG A 36 0.08 SIDE CHAIN REMARK 500 17 PHE A 94 0.08 SIDE CHAIN REMARK 500 19 ARG A 60 0.08 SIDE CHAIN REMARK 500 20 ARG A 120 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1UAP A 25 154 UNP Q15113 PCOC1_HUMAN 313 442 SEQADV 1UAP MET A 1 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP GLY A 2 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 3 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 4 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 5 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 6 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 7 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 8 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 9 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 10 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 11 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 12 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP GLY A 13 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP LEU A 14 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP VAL A 15 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP PRO A 16 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP ARG A 17 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP GLY A 18 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 19 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP HIS A 20 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP MET A 21 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP LEU A 22 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP GLU A 23 UNP Q15113 CLONING ARTIFACT SEQADV 1UAP SER A 24 UNP Q15113 CLONING ARTIFACT SEQRES 1 A 154 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 154 LEU VAL PRO ARG GLY SER HIS MET LEU GLU SER PRO ASP SEQRES 3 A 154 ALA PRO THR CYS PRO LYS GLN CYS ARG ARG THR GLY THR SEQRES 4 A 154 LEU GLN SER ASN PHE CYS ALA SER SER LEU VAL VAL THR SEQRES 5 A 154 ALA THR VAL LYS SER MET VAL ARG GLU PRO GLY GLU GLY SEQRES 6 A 154 LEU ALA VAL THR VAL SER LEU ILE GLY ALA TYR LYS THR SEQRES 7 A 154 GLY GLY LEU ASP LEU PRO SER PRO PRO THR GLY ALA SER SEQRES 8 A 154 LEU LYS PHE TYR VAL PRO CYS LYS GLN CYS PRO PRO MET SEQRES 9 A 154 LYS LYS GLY VAL SER TYR LEU LEU MET GLY GLN VAL GLU SEQRES 10 A 154 GLU ASN ARG GLY PRO VAL LEU PRO PRO GLU SER PHE VAL SEQRES 11 A 154 VAL LEU HIS ARG PRO ASN GLN ASP GLN ILE LEU THR ASN SEQRES 12 A 154 LEU SER LYS ARG LYS CYS PRO SER GLN PRO VAL HELIX 1 1 THR A 39 SER A 47 1 9 HELIX 2 2 ARG A 134 ARG A 147 1 14 SHEET 1 A 9 GLY A 74 THR A 78 0 SHEET 2 A 9 LEU A 49 ARG A 60 -1 N VAL A 50 O LYS A 77 SHEET 3 A 9 SER A 109 GLU A 117 -1 N TYR A 110 O ALA A 53 SHEET 4 A 9 PHE A 129 LEU A 132 -1 O PHE A 129 N MET A 113 SHEET 5 A 9 SER A 109 GLU A 117 -1 N LEU A 111 O VAL A 131 SHEET 6 A 9 GLY A 121 VAL A 123 -1 N GLY A 121 O GLU A 117 SHEET 7 A 9 LEU A 92 VAL A 96 1 N TYR A 95 O PRO A 122 SHEET 8 A 9 LEU A 66 VAL A 70 -1 N LEU A 66 O VAL A 96 SHEET 9 A 9 LEU A 49 ARG A 60 -1 N LYS A 56 O THR A 69 SSBOND 1 CYS A 30 CYS A 98 1555 1555 2.04 SSBOND 2 CYS A 34 CYS A 101 1555 1555 2.03 SSBOND 3 CYS A 45 CYS A 149 1555 1555 2.04 CISPEP 1 CYS A 101 PRO A 102 1 -3.62 CISPEP 2 CYS A 101 PRO A 102 2 3.21 CISPEP 3 CYS A 101 PRO A 102 3 -2.64 CISPEP 4 CYS A 101 PRO A 102 4 -1.68 CISPEP 5 CYS A 101 PRO A 102 5 2.55 CISPEP 6 CYS A 101 PRO A 102 6 -3.96 CISPEP 7 CYS A 101 PRO A 102 7 -0.07 CISPEP 8 CYS A 101 PRO A 102 8 -4.49 CISPEP 9 CYS A 101 PRO A 102 9 -1.84 CISPEP 10 CYS A 101 PRO A 102 10 1.94 CISPEP 11 CYS A 101 PRO A 102 11 -4.05 CISPEP 12 CYS A 101 PRO A 102 12 -3.32 CISPEP 13 CYS A 101 PRO A 102 13 -2.14 CISPEP 14 CYS A 101 PRO A 102 14 -4.10 CISPEP 15 CYS A 101 PRO A 102 15 -3.68 CISPEP 16 CYS A 101 PRO A 102 16 -3.96 CISPEP 17 CYS A 101 PRO A 102 17 -2.59 CISPEP 18 CYS A 101 PRO A 102 18 1.80 CISPEP 19 CYS A 101 PRO A 102 19 2.17 CISPEP 20 CYS A 101 PRO A 102 20 -3.68 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