HEADER SIGNALING PROTEIN 14-MAY-03 1PB5 TITLE NMR STRUCTURE OF A PROTOTYPE LNR MODULE FROM HUMAN NOTCH1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIRST LNR MODULE; COMPND 5 SYNONYM: NOTCH 1, HN1, TRANSLOCATION-ASSOCIATED NOTCH PROTEIN TAN-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21DE3PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMM KEYWDS NOTCH SIGNALING, LIN12/NOTCH REPEAT, CALCIUM-BINDING DOMAIN, PROTEIN KEYWDS 2 MODULE, DISULFIDE BOND, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 16 MDLTYP MINIMIZED AVERAGE AUTHOR D.VARDAR,C.L.NORTH,C.SANCHEZ-IRIZARRY,J.C.ASTER,S.C.BLACKLOW REVDAT 3 23-FEB-22 1PB5 1 REMARK LINK REVDAT 2 24-FEB-09 1PB5 1 VERSN REVDAT 1 17-JUN-03 1PB5 0 JRNL AUTH D.VARDAR,C.L.NORTH,C.SANCHEZ-IRIZARRY,J.C.ASTER,S.C.BLACKLOW JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURE OF A PROTOTYPE JRNL TITL 2 LIN12-NOTCH REPEAT MODULE FROM HUMAN NOTCH1 JRNL REF BIOCHEMISTRY V. 42 7061 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12795601 JRNL DOI 10.1021/BI034156Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, CNS 1.1 REMARK 3 AUTHORS : BRUNGER (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PB5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019211. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 6.5; 7.0 REMARK 210 IONIC STRENGTH : 10MM CA2+; 10MM CA2+, 50MM PIPES REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM LNRA U-15N, 10MM CA2+, 0.5MM REMARK 210 DSS PH 6.5; 1MM LNRA U-15N,13C, REMARK 210 10MM CA2+, 0.5MM DSS PH 6.5; REMARK 210 1.5MM LNRA U-15N,13C, 10 MM CA2+, REMARK 210 0.5MM DSS, 50 MM DEUTERATED REMARK 210 PIPES PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA, HNCOCA, 13C HSQC; 3D_15N REMARK 210 -SEPARATED TOCSY, 2D TOCSY, 15N- REMARK 210 HSQC, 15N-HMQC-J REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : DMX; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW 5.0.4, CNS 1.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION ANGLE REMARK 210 DYNAMICS, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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 H ASN A 15 OD2 ASP A 33 1.60 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 GLU A 2 87.01 -69.93 REMARK 500 1 ALA A 3 16.78 -140.86 REMARK 500 1 CYS A 4 145.02 61.56 REMARK 500 1 VAL A 17 -139.35 -95.90 REMARK 500 1 CYS A 18 109.04 -162.39 REMARK 500 1 ASP A 30 28.14 46.43 REMARK 500 2 ALA A 3 16.18 -140.25 REMARK 500 2 CYS A 4 136.91 60.68 REMARK 500 2 VAL A 17 -141.53 -96.10 REMARK 500 2 CYS A 18 105.46 -162.06 REMARK 500 2 ASP A 30 27.33 47.06 REMARK 500 3 ALA A 3 16.86 -140.44 REMARK 500 3 CYS A 4 139.95 61.68 REMARK 500 3 VAL A 17 -141.98 -97.36 REMARK 500 3 ASP A 30 23.58 48.20 REMARK 500 4 GLU A 2 58.84 -102.05 REMARK 500 4 ALA A 3 17.62 -140.41 REMARK 500 4 CYS A 4 136.08 61.38 REMARK 500 4 VAL A 17 -141.48 -97.26 REMARK 500 4 CYS A 18 105.67 -161.03 REMARK 500 4 ASP A 30 23.30 48.80 REMARK 500 5 ALA A 3 16.78 -140.37 REMARK 500 5 CYS A 4 138.63 61.30 REMARK 500 5 VAL A 17 -141.65 -97.36 REMARK 500 5 ASP A 30 23.85 47.91 REMARK 500 6 ALA A 3 17.12 -140.68 REMARK 500 6 CYS A 4 145.64 62.02 REMARK 500 6 VAL A 17 -141.43 -95.94 REMARK 500 6 CYS A 18 105.72 -160.94 REMARK 500 6 ASP A 30 23.83 47.86 REMARK 500 7 ALA A 3 17.46 -140.41 REMARK 500 7 CYS A 4 138.08 61.66 REMARK 500 7 VAL A 17 -141.58 -95.74 REMARK 500 7 CYS A 18 105.46 -161.85 REMARK 500 7 ASP A 30 26.73 47.35 REMARK 500 8 GLU A 2 44.88 -95.29 REMARK 500 8 ALA A 3 18.67 -140.57 REMARK 500 8 CYS A 4 137.17 61.89 REMARK 500 8 VAL A 17 -139.79 -97.98 REMARK 500 8 CYS A 18 105.89 -163.18 REMARK 500 8 ASP A 30 28.12 46.11 REMARK 500 9 GLU A 2 56.74 -99.53 REMARK 500 9 ALA A 3 17.43 -140.67 REMARK 500 9 CYS A 4 144.14 62.27 REMARK 500 9 VAL A 17 -139.13 -97.95 REMARK 500 9 CYS A 18 106.25 -162.58 REMARK 500 9 ASP A 30 28.00 46.01 REMARK 500 10 ALA A 3 16.87 -140.31 REMARK 500 10 CYS A 4 138.59 61.07 REMARK 500 10 VAL A 17 -139.07 -98.28 REMARK 500 REMARK 500 THIS ENTRY HAS 84 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 O REMARK 620 2 ASN A 15 OD1 70.8 REMARK 620 3 CYS A 18 N 146.1 104.0 REMARK 620 4 ASP A 30 OD1 62.9 129.3 125.9 REMARK 620 5 ASP A 30 OD2 105.2 170.9 83.9 44.1 REMARK 620 6 ASP A 33 OD2 71.1 65.0 138.7 80.9 106.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 DBREF 1PB5 A 1 35 UNP P46531 NOTC1_HUMAN 1447 1481 SEQRES 1 A 35 GLU GLU ALA CYS GLU LEU PRO GLU CYS GLN GLU ASP ALA SEQRES 2 A 35 GLY ASN LYS VAL CYS SER LEU GLN CYS ASN ASN HIS ALA SEQRES 3 A 35 CYS GLY TRP ASP GLY GLY ASP CYS SER HET CA A 501 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 GLU A 8 ALA A 13 1 6 HELIX 2 2 GLY A 28 ASP A 33 5 6 SSBOND 1 CYS A 4 CYS A 27 1555 1555 2.03 SSBOND 2 CYS A 9 CYS A 22 1555 1555 2.03 SSBOND 3 CYS A 18 CYS A 34 1555 1555 2.03 LINK O ASP A 12 CA CA A 501 1555 1555 3.09 LINK OD1 ASN A 15 CA CA A 501 1555 1555 2.31 LINK N CYS A 18 CA CA A 501 1555 1555 3.23 LINK OD1 ASP A 30 CA CA A 501 1555 1555 2.90 LINK OD2 ASP A 30 CA CA A 501 1555 1555 2.95 LINK OD2 ASP A 33 CA CA A 501 1555 1555 2.16 SITE 1 AC1 6 ASP A 12 ASN A 15 VAL A 17 CYS A 18 SITE 2 AC1 6 ASP A 30 ASP A 33 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