HEADER APOPTOSIS 11-JAN-06 2FNF TITLE C1 DOMAIN OF NORE1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE RAS EFFECTOR NORE1; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: CYSTEINE RICH DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS ZINC; SIGNAL TRANSDUCTION; APOPTOSIS; CYSTEINE RICH DOMAIN, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR E.HARJES,S.HARJES,S.WOHLGEMUTH,E.KRIEGER,C.HERRMANN,K.H.MULLER, AUTHOR 2 P.BAYER REVDAT 5 29-MAY-24 2FNF 1 REMARK REVDAT 4 09-MAR-22 2FNF 1 REMARK LINK REVDAT 3 14-APR-09 2FNF 1 JRNL REVDAT 2 24-FEB-09 2FNF 1 VERSN REVDAT 1 07-FEB-06 2FNF 0 JRNL AUTH E.HARJES,S.HARJES,S.WOHLGEMUTH,K.H.MULLER,E.KRIEGER, JRNL AUTH 2 C.HERRMANN,P.BAYER JRNL TITL GTP-RAS DISRUPTS THE INTRAMOLECULAR COMPLEX OF C1 AND RA JRNL TITL 2 DOMAINS OF NORE1. JRNL REF STRUCTURE V. 14 881 2006 JRNL REFN ISSN 0969-2126 JRNL PMID 16698549 JRNL DOI 10.1016/J.STR.2006.03.008 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AURELIA 2.8.11, YASARA 5.11.29 REMARK 3 AUTHORS : NEIDIG (AURELIA), KRIEGER (YASARA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 583 RESTRAINTS, 501 ARE REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS, 48 DIHEDRAL ANGLE RESTRAINTS, 34 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS REMARK 4 REMARK 4 2FNF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036083. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 300; 300 REMARK 210 PH : 6.9; 6.9; 6.9 REMARK 210 IONIC STRENGTH : 0.5 MM NAN3; 0.5 MM NAN3; 0.5 MM REMARK 210 NAN3 REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.6MM C1 DOMAIN UNLABELED, 20MM REMARK 210 PHOSPHATE BUFFER K; 2MM C1 REMARK 210 DOMAIN U-15N, 20MM PHOSPHATE REMARK 210 BUFFER; 2MM C1 DOMAIN U-15N/13C, REMARK 210 20MM PHOSPHATE BUFFER K REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 3D_15N-SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.5, YASARA 5.11.29 REMARK 210 METHOD USED : SIMULATED ANNEALING; MOLECULAR REMARK 210 DYNAMICS; TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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: 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: X 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-30 REMARK 465 RES C SSSEQI REMARK 465 PRO X 95 REMARK 465 ARG X 96 REMARK 465 ASP X 97 REMARK 465 VAL X 98 REMARK 465 ARG X 99 REMARK 465 SER X 100 REMARK 465 ILE X 101 REMARK 465 PHE X 102 REMARK 465 GLU X 103 REMARK 465 GLN X 104 REMARK 465 PRO X 105 REMARK 465 GLN X 106 REMARK 465 ASP X 107 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 12 THR X 152 CB THR X 152 CG2 -0.264 REMARK 500 21 CYS X 157 CB CYS X 157 SG -0.099 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 GLY X 130 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 3 GLY X 130 N - CA - C ANGL. DEV. = -19.0 DEGREES REMARK 500 5 LYS X 150 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 7 GLY X 130 N - CA - C ANGL. DEV. = -15.7 DEGREES REMARK 500 12 THR X 152 N - CA - CB ANGL. DEV. = -12.2 DEGREES REMARK 500 13 GLY X 117 N - CA - C ANGL. DEV. = -16.0 DEGREES REMARK 500 13 GLY X 130 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 15 GLY X 130 N - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 16 GLY X 130 N - CA - C ANGL. DEV. = -18.2 DEGREES REMARK 500 16 ASP X 164 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 17 LYS X 150 N - CA - C ANGL. DEV. = 18.7 DEGREES REMARK 500 18 GLY X 130 N - CA - C ANGL. DEV. = -20.0 DEGREES REMARK 500 18 LYS X 150 N - CA - C ANGL. DEV. = 20.5 DEGREES REMARK 500 20 GLY X 130 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 21 LYS X 150 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 22 PHE X 151 N - CA - C ANGL. DEV. = 19.3 DEGREES REMARK 500 24 GLY X 130 N - CA - C ANGL. DEV. = -18.0 DEGREES REMARK 500 25 GLY X 130 N - CA - C ANGL. DEV. = -15.0 DEGREES REMARK 500 26 GLY X 130 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 27 GLY X 130 N - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 28 GLY X 130 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 29 GLY X 130 N - CA - C ANGL. DEV. = -15.2 DEGREES REMARK 500 30 GLY X 130 N - CA - C ANGL. DEV. = -19.2 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 ARG X 126 36.43 -63.91 REMARK 500 1 PRO X 129 -177.28 -62.70 REMARK 500 1 CYS X 149 -51.71 -169.18 REMARK 500 1 LYS X 150 -120.79 -80.30 REMARK 500 1 ASP X 164 -176.39 -61.60 REMARK 500 2 VAL X 110 32.19 -92.77 REMARK 500 2 GLU X 113 -4.54 -58.54 REMARK 500 2 GLU X 116 33.87 -74.25 REMARK 500 2 ALA X 124 25.43 -64.66 REMARK 500 2 CYS X 149 -54.74 -161.75 REMARK 500 2 LYS X 150 -119.58 -98.70 REMARK 500 2 ASP X 164 -179.41 -53.75 REMARK 500 3 VAL X 110 49.03 -89.54 REMARK 500 3 ALA X 124 47.56 -86.21 REMARK 500 3 VAL X 139 78.92 -105.80 REMARK 500 3 GLN X 142 78.65 -66.12 REMARK 500 3 CYS X 149 -47.89 -165.15 REMARK 500 3 LYS X 150 -129.05 -89.47 REMARK 500 3 ASP X 164 -179.37 -66.12 REMARK 500 4 LEU X 111 39.59 -76.01 REMARK 500 4 VAL X 121 96.65 -67.86 REMARK 500 4 CYS X 149 -49.15 -164.55 REMARK 500 4 LYS X 150 -122.25 -95.30 REMARK 500 4 ASP X 164 -177.52 -55.44 REMARK 500 5 ALA X 124 42.32 -89.27 REMARK 500 5 LEU X 125 51.47 -67.69 REMARK 500 5 PRO X 129 -166.45 -67.09 REMARK 500 5 CYS X 149 -54.88 -163.79 REMARK 500 5 LYS X 150 -88.90 -107.43 REMARK 500 6 GLU X 113 49.81 -83.23 REMARK 500 6 HIS X 118 100.13 -52.41 REMARK 500 6 ALA X 124 38.70 -93.05 REMARK 500 6 LEU X 125 47.74 -68.08 REMARK 500 6 CYS X 149 -51.97 -161.36 REMARK 500 6 LYS X 150 -88.50 -101.71 REMARK 500 6 ASP X 164 -179.55 -62.07 REMARK 500 7 GLU X 116 53.14 -68.08 REMARK 500 7 ALA X 124 47.78 -73.66 REMARK 500 7 ARG X 126 39.58 -71.63 REMARK 500 7 GLN X 142 90.99 -68.65 REMARK 500 7 CYS X 149 -39.28 -168.71 REMARK 500 7 LYS X 150 -122.28 -85.54 REMARK 500 7 ASP X 164 -179.30 -57.35 REMARK 500 8 ARG X 114 -164.61 -70.15 REMARK 500 8 ARG X 126 -126.04 60.27 REMARK 500 8 CYS X 149 -50.89 -161.96 REMARK 500 8 LYS X 150 -120.29 -98.53 REMARK 500 8 ASP X 164 -179.50 -55.25 REMARK 500 9 LEU X 125 -142.99 -104.83 REMARK 500 9 ARG X 126 -0.69 66.33 REMARK 500 REMARK 500 THIS ENTRY HAS 173 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 3 GLU X 116 0.09 SIDE CHAIN REMARK 500 8 GLU X 116 0.07 SIDE CHAIN REMARK 500 11 GLU X 116 0.07 SIDE CHAIN REMARK 500 11 ASP X 164 0.08 SIDE CHAIN REMARK 500 16 ASP X 164 0.07 SIDE CHAIN REMARK 500 25 GLU X 122 0.07 SIDE CHAIN REMARK 500 25 GLU X 156 0.09 SIDE CHAIN REMARK 500 26 GLU X 156 0.07 SIDE CHAIN REMARK 500 28 GLU X 122 0.07 SIDE CHAIN REMARK 500 30 GLU X 156 0.07 SIDE CHAIN 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 X 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS X 132 SG REMARK 620 2 CYS X 135 SG 110.5 REMARK 620 3 HIS X 154 ND1 94.6 120.1 REMARK 620 4 CYS X 157 SG 136.5 101.6 93.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN X 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS X 118 ND1 REMARK 620 2 CYS X 146 SG 88.5 REMARK 620 3 CYS X 149 SG 104.4 106.2 REMARK 620 4 CYS X 165 SG 107.3 106.6 134.4 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 X 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN X 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RFH RELATED DB: PDB REMARK 900 THE SAME STRUCTURE OF THE SAME PROTEIN CALCULATED WITH CNS DBREF 2FNF X 95 166 GB 2997698 AAC08580 95 166 SEQRES 1 X 72 PRO ARG ASP VAL ARG SER ILE PHE GLU GLN PRO GLN ASP SEQRES 2 X 72 PRO ARG VAL LEU ALA GLU ARG GLY GLU GLY HIS ARG PHE SEQRES 3 X 72 VAL GLU LEU ALA LEU ARG GLY GLY PRO GLY TRP CYS ASP SEQRES 4 X 72 LEU CYS GLY ARG GLU VAL LEU ARG GLN ALA LEU ARG CYS SEQRES 5 X 72 ALA ASN CYS LYS PHE THR CYS HIS SER GLU CYS ARG SER SEQRES 6 X 72 LEU ILE GLN LEU ASP CYS ARG HET ZN X 1 1 HET ZN X 2 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 LEU X 111 GLY X 115 5 5 HELIX 2 2 SER X 155 ILE X 161 5 7 SHEET 1 A 3 VAL X 121 GLU X 122 0 SHEET 2 A 3 LEU X 144 ARG X 145 -1 O ARG X 145 N VAL X 121 SHEET 3 A 3 THR X 152 CYS X 153 -1 O CYS X 153 N LEU X 144 LINK ZN ZN X 1 SG CYS X 132 1555 1555 2.15 LINK ZN ZN X 1 SG CYS X 135 1555 1555 2.13 LINK ZN ZN X 1 ND1 HIS X 154 1555 1555 2.20 LINK ZN ZN X 1 SG CYS X 157 1555 1555 2.15 LINK ZN ZN X 2 ND1 HIS X 118 1555 1555 2.11 LINK ZN ZN X 2 SG CYS X 146 1555 1555 2.28 LINK ZN ZN X 2 SG CYS X 149 1555 1555 2.18 LINK ZN ZN X 2 SG CYS X 165 1555 1555 2.10 SITE 1 AC1 4 CYS X 132 CYS X 135 HIS X 154 CYS X 157 SITE 1 AC2 5 HIS X 118 CYS X 146 ASN X 148 CYS X 149 SITE 2 AC2 5 CYS X 165 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