HEADER MEMBRANE PROTEIN 10-JUN-09 2KJX TITLE SOLUTION STRUCTURE OF THE EXTRACELLULAR DOMAIN OF JTB COMPND MOL_ID: 1; COMPND 2 MOLECULE: JUMPING TRANSLOCATION BREAKPOINT PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN (UNP RESIDUES 47-104); COMPND 5 SYNONYM: PROTEIN JTB, PROSTATE ANDROGEN-REGULATED PROTEIN, PAR COMPND 6 PROTEIN; COMPND 7 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: JTB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32A KEYWDS CYSTEINE-RICH DOMAIN, MEMBRANE, TRANSMEMBRANE, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.ROUSSEAU,A.LINGEL,B.PAN,W.J.FAIRBROTHER,F.BAZAN REVDAT 4 30-OCT-24 2KJX 1 REMARK SEQADV REVDAT 3 18-APR-12 2KJX 1 JRNL REVDAT 2 23-NOV-11 2KJX 1 JRNL VERSN REVDAT 1 11-AUG-10 2KJX 0 JRNL AUTH F.ROUSSEAU,B.PAN,W.J.FAIRBROTHER,J.F.BAZAN,A.LINGEL JRNL TITL THE STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE JUMPING JRNL TITL 2 TRANSLOCATION BREAKPOINT PROTEIN REVEALS A VARIATION OF THE JRNL TITL 3 MIDKINE FOLD. JRNL REF J.MOL.BIOL. V. 415 22 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22079049 JRNL DOI 10.1016/J.JMB.2011.10.048 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, CNS REMARK 3 AUTHORS : BRUKER (TOPSPIN), BRUNGER, ADAMS, CLORE, GROS, REMARK 3 NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE RESTRAINTS WERE DERIVED FROM REMARK 3 15N- OR 13C-RESOLVED 3D NOESY EXPERIMENTS AND A 2D HOMONUCLEAR REMARK 3 1H NOESY EXPERIMENT. RESTRAINTS FOR THE BACKBONE ANGLES PHI AND REMARK 3 PSI WERE DERIVED FROM 3J(HN,HA) COUPLING CONSTANTS AND TALOS. REMARK 3 STEREOSPECIFIC ASSIGNMENTS OF LEU, VAL METHYL GROUPS WERE REMARK 3 OBTAINED USING A 10% FRACTIONALLY 13C-LABELED SAMPLE. FOR THE REMARK 3 DEFINITION OF H-BONDS, SLOWLY EXCHANGING AMIDE PROTONS WERE REMARK 3 IDENTIFIED FROM 1H, 15N CORRELATION EXPERIMENTS AFTER REMARK 3 REDISSOLVING LYOPHILIZED PROTEIN IN D2O. REMARK 4 REMARK 4 2KJX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101212. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.6 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] JTB, 50 MM REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.1 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] JTB, 50 MM REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.1 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O; 1 MM JTB, 50 MM REMARK 210 SODIUM PHOSPHATE, 150 MM SODIUM REMARK 210 CHLORIDE, 0.1 MM SODIUM AZIDE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNHA; REMARK 210 3D HNHB; 3D H(CCO)NH; 3D C(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D HBHA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPN, TALOS, CNS REMARK 210 METHOD USED : 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 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 VAL A 17 93.66 -58.97 REMARK 500 1 GLU A 20 156.12 -48.88 REMARK 500 1 PRO A 23 157.81 -46.54 REMARK 500 1 SER A 25 -177.67 -54.03 REMARK 500 1 LYS A 50 73.83 42.47 REMARK 500 1 GLU A 63 89.91 -150.56 REMARK 500 2 VAL A 17 93.73 -58.84 REMARK 500 2 GLU A 20 158.17 -48.81 REMARK 500 2 PRO A 23 159.65 -49.07 REMARK 500 2 SER A 25 -169.45 -57.31 REMARK 500 2 PRO A 37 -78.72 -76.99 REMARK 500 2 LYS A 50 73.83 42.25 REMARK 500 2 GLU A 63 89.88 -154.98 REMARK 500 3 GLU A 6 139.95 -174.85 REMARK 500 3 VAL A 17 93.80 -58.96 REMARK 500 3 GLU A 20 152.70 -48.88 REMARK 500 3 PRO A 23 158.30 -47.27 REMARK 500 3 SER A 25 -175.35 -57.97 REMARK 500 3 LYS A 50 73.94 42.18 REMARK 500 4 SER A 2 -74.60 -160.53 REMARK 500 4 VAL A 17 93.67 -58.96 REMARK 500 4 GLU A 20 160.64 -48.74 REMARK 500 4 PRO A 23 160.17 -44.06 REMARK 500 4 SER A 25 -173.22 -57.09 REMARK 500 4 SER A 49 8.44 80.34 REMARK 500 4 LYS A 50 73.88 42.24 REMARK 500 4 GLU A 63 89.94 -154.91 REMARK 500 5 VAL A 17 94.01 -58.92 REMARK 500 5 GLU A 20 169.79 -48.88 REMARK 500 5 PRO A 23 158.70 -45.11 REMARK 500 5 SER A 25 -167.16 -60.52 REMARK 500 5 LYS A 30 -63.02 -92.11 REMARK 500 5 GLU A 34 32.62 -89.83 REMARK 500 5 PRO A 37 -83.40 -76.17 REMARK 500 5 SER A 49 -13.11 105.28 REMARK 500 5 LYS A 50 74.05 48.66 REMARK 500 6 SER A 2 105.67 -168.60 REMARK 500 6 VAL A 17 93.56 -58.94 REMARK 500 6 GLU A 20 163.72 -48.72 REMARK 500 6 PRO A 23 160.84 -46.08 REMARK 500 6 SER A 25 -175.46 -54.60 REMARK 500 6 SER A 49 8.48 80.08 REMARK 500 6 LYS A 50 73.79 42.25 REMARK 500 6 GLU A 63 89.99 -153.78 REMARK 500 7 VAL A 17 93.95 -58.81 REMARK 500 7 GLU A 20 170.46 -48.80 REMARK 500 7 PRO A 23 161.23 -47.29 REMARK 500 7 SER A 25 -173.92 -62.59 REMARK 500 7 LYS A 30 -63.15 -92.32 REMARK 500 7 GLU A 34 40.59 -89.19 REMARK 500 REMARK 500 THIS ENTRY HAS 153 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16331 RELATED DB: BMRB DBREF 2KJX A 8 65 UNP O76095 JTB_HUMAN 47 104 SEQADV 2KJX GLY A 1 UNP O76095 EXPRESSION TAG SEQADV 2KJX SER A 2 UNP O76095 EXPRESSION TAG SEQADV 2KJX GLY A 3 UNP O76095 EXPRESSION TAG SEQADV 2KJX MET A 4 UNP O76095 EXPRESSION TAG SEQADV 2KJX LYS A 5 UNP O76095 EXPRESSION TAG SEQADV 2KJX GLU A 6 UNP O76095 EXPRESSION TAG SEQADV 2KJX PHE A 7 UNP O76095 EXPRESSION TAG SEQRES 1 A 65 GLY SER GLY MET LYS GLU PHE PRO CYS TRP LEU VAL GLU SEQRES 2 A 65 GLU PHE VAL VAL ALA GLU GLU CYS SER PRO CYS SER ASN SEQRES 3 A 65 PHE ARG ALA LYS THR THR PRO GLU CYS GLY PRO THR GLY SEQRES 4 A 65 TYR VAL GLU LYS ILE THR CYS SER SER SER LYS ARG ASN SEQRES 5 A 65 GLU PHE LYS SER CYS ARG SER ALA LEU MET GLU GLN ARG HELIX 1 1 ASN A 26 THR A 31 1 6 SHEET 1 A 3 PHE A 15 PRO A 23 0 SHEET 2 A 3 TYR A 40 CYS A 46 -1 O LYS A 43 N GLU A 19 SHEET 3 A 3 ARG A 51 SER A 56 -1 O GLU A 53 N ILE A 44 SSBOND 1 CYS A 9 CYS A 46 1555 1555 2.03 SSBOND 2 CYS A 21 CYS A 57 1555 1555 2.03 SSBOND 3 CYS A 24 CYS A 35 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