HEADER TOXIN 19-SEP-07 2JVE TITLE SOLUTION STRUCTURE OF THE EXTRACELLULAR DOMAIN OF PROD1, A PROTEIN TITLE 2 IMPLICATED IN PROXIMODISTAL IDENTITY DURING AMPHIBIAN LIMB TITLE 3 REGENERATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROD 1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOTOPHTHALMUS VIRIDESCENS; SOURCE 3 ORGANISM_COMMON: RED-SPOTTED NEWT; SOURCE 4 ORGANISM_TAXID: 8316; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS LY-6, THREE-FINGER SNAKE TOXIN, UPAR, CD59, LIMB REGENERATION, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.GARZA-GARCIA,R.HARRIS,D.ESPOSITO,P.C.DRISCOLL REVDAT 5 14-JUN-23 2JVE 1 REMARK REVDAT 4 19-FEB-20 2JVE 1 REMARK SEQADV REVDAT 3 19-DEC-12 2JVE 1 JRNL DBREF SEQADV SOURCE REVDAT 3 2 1 VERSN REVDAT 2 24-FEB-09 2JVE 1 VERSN REVDAT 1 30-SEP-08 2JVE 0 JRNL AUTH A.GARZA-GARCIA,R.HARRIS,D.ESPOSITO,P.B.GATES,P.C.DRISCOLL JRNL TITL SOLUTION STRUCTURE AND PHYLOGENETICS OF PROD1, A MEMBER OF JRNL TITL 2 THE THREE-FINGER PROTEIN SUPERFAMILY IMPLICATED IN JRNL TITL 3 SALAMANDER LIMB REGENERATION. JRNL REF PLOS ONE V. 4 E7123 2009 JRNL REFN ESSN 1932-6203 JRNL PMID 19771161 JRNL DOI 10.1371/JOURNAL.PONE.0007123 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, F. ET AL. (NMRPIPE), SCHWIETERS, C.D. ET REMARK 3 AL. (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED USING AN REMARK 3 AB-INITIO SIMULATED ANNEALING PROTOCOL WITHIN THE CNS/XPLOR-NIH REMARK 3 PROGRAMS WITH PARALLHDG V5.3 PARAMETER SET AND PROLSQ NON-BONDED REMARK 3 ENERGY FUNCTION. CARTESIAN AND TORSION ANGLE DYNAMICS WERE USED REMARK 3 TO REFINE THE STRUCTURES. REMARK 4 REMARK 4 2JVE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000100338. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] PROD1, 50 MM SODIUM REMARK 210 PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 90% H2O/10% REMARK 210 D2O; 1 MM [U-13C; U-15N] PROD1, REMARK 210 50 MM SODIUM PHOSPHATE, 150 MM REMARK 210 SODIUM CHLORIDE, 1 MM EDTA, 90% REMARK 210 H2O/10% D2O; 1 MM [U-13C; U-15N] REMARK 210 PROD1, 50 MM SODIUM PHOSPHATE, REMARK 210 150 MM SODIUM CHLORIDE, 1 MM REMARK 210 EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C AROMATIC NOESY; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D HN(CA)CO; REMARK 210 3D HA(CA)NH; 3D HN(CACO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HCCH-COSY; 3D 1H- REMARK 210 15N TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 SER A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 LEU A 11 REMARK 465 VAL A 12 REMARK 465 PRO A 13 REMARK 465 ARG A 14 REMARK 465 GLY A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 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 OE1 GLU A 54 HZ2 LYS A 56 1.52 REMARK 500 HH21 ARG A 25 OD1 ASP A 28 1.56 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 ALA A 19 107.76 67.40 REMARK 500 1 TYR A 49 -59.35 -139.02 REMARK 500 1 SER A 50 -150.08 -121.62 REMARK 500 1 GLU A 80 153.17 177.63 REMARK 500 1 SER A 86 -60.81 -153.98 REMARK 500 1 GLU A 87 33.87 -83.58 REMARK 500 2 TYR A 49 -65.39 -125.00 REMARK 500 3 TYR A 49 -44.43 -138.35 REMARK 500 3 SER A 50 -151.39 -150.77 REMARK 500 3 GLU A 54 146.10 -174.03 REMARK 500 3 GLU A 80 152.04 179.64 REMARK 500 3 ASN A 84 -81.45 -60.09 REMARK 500 3 ARG A 85 -123.73 31.96 REMARK 500 4 ASP A 28 -53.37 -125.21 REMARK 500 4 GLU A 80 145.08 173.45 REMARK 500 5 ALA A 19 175.38 67.08 REMARK 500 5 ASP A 28 -83.21 -77.73 REMARK 500 5 GLN A 39 59.31 -95.50 REMARK 500 5 TYR A 49 -45.98 -141.15 REMARK 500 5 GLU A 80 147.36 175.25 REMARK 500 6 ASP A 28 -34.85 -140.83 REMARK 500 6 PRO A 48 28.54 -75.19 REMARK 500 6 TYR A 49 -26.02 -172.13 REMARK 500 6 SER A 50 -153.31 -149.70 REMARK 500 6 GLU A 80 150.79 171.26 REMARK 500 6 ASN A 84 40.61 -82.82 REMARK 500 7 ALA A 19 87.28 57.05 REMARK 500 7 SER A 50 -163.92 -169.57 REMARK 500 7 GLU A 80 137.64 175.13 REMARK 500 8 GLN A 39 78.54 -101.10 REMARK 500 8 SER A 50 -154.95 -169.36 REMARK 500 8 GLU A 80 141.46 176.85 REMARK 500 9 TYR A 49 -55.75 -136.55 REMARK 500 9 GLU A 80 148.73 174.81 REMARK 500 10 ALA A 19 154.89 178.28 REMARK 500 10 GLN A 39 52.39 -110.10 REMARK 500 10 THR A 40 25.64 -79.85 REMARK 500 10 SER A 50 -162.09 -161.67 REMARK 500 10 GLU A 80 142.15 179.06 REMARK 500 11 TYR A 49 -48.31 -160.46 REMARK 500 11 SER A 50 -153.17 -120.55 REMARK 500 11 GLU A 80 161.72 177.22 REMARK 500 12 ASP A 28 -45.16 -150.20 REMARK 500 12 GLU A 80 144.16 173.74 REMARK 500 13 ASP A 28 -87.45 -144.57 REMARK 500 13 TYR A 49 -64.56 -128.38 REMARK 500 13 GLU A 80 149.79 171.53 REMARK 500 13 ASN A 84 37.77 -78.36 REMARK 500 13 GLU A 87 81.01 52.94 REMARK 500 14 GLN A 39 72.78 -102.44 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15477 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE IS NOT AVAILABLE AT UNIPROT DATABASE AT THE REMARK 999 TIME OF PROCESSING. DBREF 2JVE A 19 88 UNP A8D0E6 A8D0E6_NOTVI 19 88 SEQADV 2JVE MET A -2 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE GLY A -1 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE SER A 0 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE SER A 1 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 2 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 3 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 4 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 5 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 6 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 7 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE SER A 8 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE SER A 9 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE GLY A 10 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE LEU A 11 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE VAL A 12 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE PRO A 13 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE ARG A 14 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE GLY A 15 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE SER A 16 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE HIS A 17 UNP A8D0E6 EXPRESSION TAG SEQADV 2JVE MET A 18 UNP A8D0E6 EXPRESSION TAG SEQRES 1 A 91 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 91 LEU VAL PRO ARG GLY SER HIS MET ALA LEU LYS CYS PHE SEQRES 3 A 91 THR ARG ASN GLY ASP ASP ARG THR VAL THR THR CYS ALA SEQRES 4 A 91 GLU GLU GLN THR ARG CYS LEU PHE VAL GLN LEU PRO TYR SEQRES 5 A 91 SER GLU ILE GLN GLU CYS LYS THR VAL GLN GLN CYS ALA SEQRES 6 A 91 GLU VAL LEU GLU GLU VAL THR ALA ILE GLY TYR PRO ALA SEQRES 7 A 91 LYS CYS CYS CYS GLU ASP LEU CYS ASN ARG SER GLU GLN HELIX 1 1 THR A 57 ALA A 70 1 14 SHEET 1 A 2 LEU A 20 THR A 24 0 SHEET 2 A 2 THR A 31 CYS A 35 -1 O CYS A 35 N LEU A 20 SHEET 1 B 3 GLU A 51 LYS A 56 0 SHEET 2 B 3 ARG A 41 GLN A 46 -1 N LEU A 43 O GLU A 54 SHEET 3 B 3 ALA A 75 CYS A 78 -1 O LYS A 76 N PHE A 44 SSBOND 1 CYS A 22 CYS A 42 1555 1555 2.03 SSBOND 2 CYS A 35 CYS A 55 1555 1555 2.03 SSBOND 3 CYS A 61 CYS A 77 1555 1555 2.03 SSBOND 4 CYS A 78 CYS A 83 1555 1555 2.03 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