PDB Short entry for 1JNP HEADER IMMUNE SYSTEM 24-JUL-01 1JNP TITLE CRYSTAL STRUCTURE OF MURINE TCL1 AT 2.5 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: P14 TCL1 PROTEIN, TCL1 ONCOGENE, TCL-1 PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 KEYWDS BETA BARREL, DIMER, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.M.PETOCK,I.Y.TORSHIN,Y.F.WANG,G.C.DUBOIS,C.M.CROCE,R.W.HARRISON, AUTHOR 2 I.T.WEBER REVDAT 6 07-FEB-24 1JNP 1 REMARK REVDAT 5 27-OCT-21 1JNP 1 REMARK SEQADV REVDAT 4 31-JAN-18 1JNP 1 REMARK REVDAT 3 24-FEB-09 1JNP 1 VERSN REVDAT 2 01-APR-03 1JNP 1 JRNL REVDAT 1 07-NOV-01 1JNP 0 JRNL AUTH J.M.PETOCK,I.Y.TORSHIN,Y.F.WANG,G.C.DU BOIS,C.M.CROCE, JRNL AUTH 2 R.W.HARRISON,I.T.WEBER JRNL TITL STRUCTURE OF MURINE TCL1 AT 2.5 A RESOLUTION AND JRNL TITL 2 IMPLICATIONS FOR THE TCL ONCOGENE FAMILY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 57 1545 2001 JRNL REFN ISSN 0907-4449 JRNL PMID 11679718 JRNL DOI 10.1107/S090744490101352X REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.226 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.196 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 606 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11625 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.189 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 502 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 9281 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1752 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 49 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1803.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1813 REMARK 3 NUMBER OF RESTRAINTS : 2096 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.000 REMARK 3 ANGLE DISTANCES (A) : 0.000 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.048 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.094 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-01. REMARK 100 THE DEPOSITION ID IS D_1000013979. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 3.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.037 REMARK 200 MONOCHROMATOR : DOUBLE FLAT CRYSTAL FIXED-EXIT REMARK 200 MONOCHROMATOR, SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11802 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26400 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, TRIS, 1-O-OCTYL-BETA-D REMARK 280 -GLUCOPYRANOSIDE, PH 3.9, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.66150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.95550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.66150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.95550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 ALA A 6 REMARK 465 HIS A 7 REMARK 465 ILE A 109 REMARK 465 ASP A 110 REMARK 465 SER A 111 REMARK 465 GLU A 112 REMARK 465 SER A 113 REMARK 465 ASN A 114 REMARK 465 ASP A 115 REMARK 465 GLU A 116 REMARK 465 MET B 201 REMARK 465 ALA B 202 REMARK 465 THR B 203 REMARK 465 GLN B 204 REMARK 465 ARG B 205 REMARK 465 ALA B 206 REMARK 465 HIS B 207 REMARK 465 ILE B 309 REMARK 465 ASP B 310 REMARK 465 SER B 311 REMARK 465 GLU B 312 REMARK 465 SER B 313 REMARK 465 ASN B 314 REMARK 465 ASP B 315 REMARK 465 GLU B 316 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 VAL B 266 CB CG1 CG2 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 HIS A 24 C - N - CA ANGL. DEV. = 27.8 DEGREES REMARK 500 VAL A 66 C - N - CA 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 PRO A 12 -82.16 -59.09 REMARK 500 TRP A 21 -65.80 -96.28 REMARK 500 ASP A 28 -168.38 -109.24 REMARK 500 ASN A 42 -30.49 -146.52 REMARK 500 GLU A 43 -59.20 -151.87 REMARK 500 GLU A 58 83.84 76.22 REMARK 500 ALA A 59 106.77 -54.46 REMARK 500 LEU A 65 -78.29 -107.57 REMARK 500 VAL A 66 -48.13 -148.44 REMARK 500 ASP A 86 46.33 -105.23 REMARK 500 ARG A 99 80.33 58.75 REMARK 500 ALA B 209 86.21 -162.00 REMARK 500 GLU B 243 -25.48 -172.95 REMARK 500 GLU B 252 110.65 178.74 REMARK 500 GLU B 258 113.52 -38.97 REMARK 500 VAL B 266 156.03 56.79 REMARK 500 PRO B 267 104.34 -37.07 REMARK 500 ASP B 280 -6.48 158.26 REMARK 500 ALA B 285 62.47 -61.80 REMARK 500 ASP B 286 17.07 175.37 REMARK 500 ARG B 299 73.98 67.02 REMARK 500 ASP B 300 17.83 59.41 REMARK 500 REMARK 500 REMARK: NULL DBREF 1JNP A 1 116 UNP P56280 TCL1A_MOUSE 1 116 DBREF 1JNP B 201 316 UNP P56280 TCL1A_MOUSE 1 116 SEQADV 1JNP ALA A 85 UNP P56280 CYS 85 ENGINEERED MUTATION SEQADV 1JNP ALA B 285 UNP P56280 CYS 85 ENGINEERED MUTATION SEQRES 1 A 116 MET ALA THR GLN ARG ALA HIS ARG ALA GLU THR PRO ALA SEQRES 2 A 116 HIS PRO ASN ARG LEU TRP ILE TRP GLU LYS HIS VAL TYR SEQRES 3 A 116 LEU ASP GLU PHE ARG ARG SER TRP LEU PRO VAL VAL ILE SEQRES 4 A 116 LYS SER ASN GLU LYS PHE GLN VAL ILE LEU ARG GLN GLU SEQRES 5 A 116 ASP VAL THR LEU GLY GLU ALA MET SER PRO SER GLN LEU SEQRES 6 A 116 VAL PRO TYR GLU LEU PRO LEU MET TRP GLN LEU TYR PRO SEQRES 7 A 116 LYS ASP ARG TYR ARG SER ALA ASP SER MET TYR TRP GLN SEQRES 8 A 116 ILE LEU TYR HIS ILE LYS PHE ARG ASP VAL GLU ASP MET SEQRES 9 A 116 LEU LEU GLU LEU ILE ASP SER GLU SER ASN ASP GLU SEQRES 1 B 116 MET ALA THR GLN ARG ALA HIS ARG ALA GLU THR PRO ALA SEQRES 2 B 116 HIS PRO ASN ARG LEU TRP ILE TRP GLU LYS HIS VAL TYR SEQRES 3 B 116 LEU ASP GLU PHE ARG ARG SER TRP LEU PRO VAL VAL ILE SEQRES 4 B 116 LYS SER ASN GLU LYS PHE GLN VAL ILE LEU ARG GLN GLU SEQRES 5 B 116 ASP VAL THR LEU GLY GLU ALA MET SER PRO SER GLN LEU SEQRES 6 B 116 VAL PRO TYR GLU LEU PRO LEU MET TRP GLN LEU TYR PRO SEQRES 7 B 116 LYS ASP ARG TYR ARG SER ALA ASP SER MET TYR TRP GLN SEQRES 8 B 116 ILE LEU TYR HIS ILE LYS PHE ARG ASP VAL GLU ASP MET SEQRES 9 B 116 LEU LEU GLU LEU ILE ASP SER GLU SER ASN ASP GLU FORMUL 3 HOH *49(H2 O) HELIX 1 1 SER B 261 VAL B 266 1 6 SHEET 1 A 8 LEU A 18 ILE A 20 0 SHEET 2 A 8 TYR A 26 ASP A 28 -1 O LEU A 27 N TRP A 19 SHEET 3 A 8 SER A 33 LYS A 40 -1 O TRP A 34 N TYR A 26 SHEET 4 A 8 GLN A 46 GLN A 51 -1 N GLN A 46 O LYS A 40 SHEET 5 A 8 ASP A 103 GLU A 107 -1 O MET A 104 N LEU A 49 SHEET 6 A 8 TYR A 89 TYR A 94 -1 N GLN A 91 O GLU A 107 SHEET 7 A 8 TYR A 82 SER A 84 -1 O TYR A 82 N TRP A 90 SHEET 8 A 8 TRP A 74 LEU A 76 -1 N GLN A 75 O ARG A 83 SHEET 1 B 9 ARG B 217 GLU B 222 0 SHEET 2 B 9 VAL B 225 LEU B 227 -1 O VAL B 225 N TRP B 221 SHEET 3 B 9 SER B 233 ILE B 239 -1 N TRP B 234 O TYR B 226 SHEET 4 B 9 GLN B 246 GLN B 251 -1 N ILE B 248 O VAL B 238 SHEET 5 B 9 GLU B 302 GLU B 307 -1 O GLU B 302 N GLN B 251 SHEET 6 B 9 TYR B 289 LYS B 297 -1 N GLN B 291 O GLU B 307 SHEET 7 B 9 TYR B 282 SER B 284 -1 O TYR B 282 N TRP B 290 SHEET 8 B 9 MET B 273 LEU B 276 -1 O GLN B 275 N ARG B 283 SHEET 9 B 9 ARG B 217 GLU B 222 -1 O LEU B 218 N TRP B 274 CISPEP 1 VAL A 54 THR A 55 0 -0.47 CISPEP 2 LEU A 65 VAL A 66 0 -0.02 CRYST1 89.323 115.911 37.945 90.00 115.15 90.00 C 1 2 1 8 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 0.011195 0.000000 0.005256 0.00000 SCALE2 0.000000 0.008627 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029114 0.00000