PDB Short entry for 4NAD HEADER TRANSCRIPTION 22-OCT-13 4NAD TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF CREPT COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN COMPND 3 1B; COMPND 4 CHAIN: B, A; COMPND 5 FRAGMENT: UNP RESIDUES 177-326; COMPND 6 SYNONYM: CELL CYCLE-RELATED AND EXPRESSION-ELEVATED PROTEIN IN TUMOR; 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: RPRD1B, C20ORF77, CREPT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS COILED-COIL, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.MEI,Z.JIN,F.REN,Y.WANG REVDAT 2 20-MAR-24 4NAD 1 SEQADV REVDAT 1 11-DEC-13 4NAD 0 JRNL AUTH K.MEI,Z.JIN,F.REN,Y.WANG,Z.CHANG,X.WANG JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF CREPT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 14346 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 42.1757 - 4.7863 0.94 2638 142 0.1837 0.2040 REMARK 3 2 4.7863 - 3.7998 0.97 2748 142 0.2180 0.3160 REMARK 3 3 3.7998 - 3.3197 0.97 2770 129 0.2713 0.3460 REMARK 3 4 3.3197 - 3.0163 0.97 2754 129 0.3322 0.3777 REMARK 3 5 3.0163 - 2.8001 0.97 2790 104 0.3525 0.4178 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.410 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 70.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.78 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 2114 REMARK 3 ANGLE : 1.565 2836 REMARK 3 CHIRALITY : 0.077 338 REMARK 3 PLANARITY : 0.007 368 REMARK 3 DIHEDRAL : 19.755 848 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE ENTRY CONTAINS FRIEDEL PAIRS IN REMARK 3 I(F)_PLUS/MINUS COLUMNS REMARK 4 REMARK 4 4NAD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-13. REMARK 100 THE DEPOSITION ID IS D_1000082952. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97927 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14346 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.171 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 3350, PH 5.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 27.83000 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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. (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 LEU B 306 REMARK 465 PRO B 307 REMARK 465 ASN B 308 REMARK 465 VAL B 309 REMARK 465 THR B 310 REMARK 465 GLY B 311 REMARK 465 GLY B 312 REMARK 465 LEU B 313 REMARK 465 ALA B 314 REMARK 465 PRO B 315 REMARK 465 LEU B 316 REMARK 465 PRO B 317 REMARK 465 SER B 318 REMARK 465 ALA B 319 REMARK 465 GLY B 320 REMARK 465 ASP B 321 REMARK 465 LEU B 322 REMARK 465 PHE B 323 REMARK 465 SER B 324 REMARK 465 THR B 325 REMARK 465 ASP B 326 REMARK 465 LEU A 306 REMARK 465 PRO A 307 REMARK 465 ASN A 308 REMARK 465 VAL A 309 REMARK 465 THR A 310 REMARK 465 GLY A 311 REMARK 465 GLY A 312 REMARK 465 LEU A 313 REMARK 465 ALA A 314 REMARK 465 PRO A 315 REMARK 465 LEU A 316 REMARK 465 PRO A 317 REMARK 465 SER A 318 REMARK 465 ALA A 319 REMARK 465 GLY A 320 REMARK 465 ASP A 321 REMARK 465 LEU A 322 REMARK 465 PHE A 323 REMARK 465 SER A 324 REMARK 465 THR A 325 REMARK 465 ASP A 326 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 MET B 174 132.47 -170.24 REMARK 500 SER B 176 128.67 105.72 REMARK 500 ASN B 189 35.61 -88.17 REMARK 500 SER B 192 -73.71 -49.89 REMARK 500 ASP B 194 -82.42 -33.95 REMARK 500 SER B 299 0.93 -168.10 REMARK 500 SER B 304 60.98 -173.21 REMARK 500 ASN A 189 36.40 -90.91 REMARK 500 ALA A 191 -103.89 -83.61 REMARK 500 SER A 192 -96.81 48.94 REMARK 500 ASP A 194 -82.78 -49.52 REMARK 500 SER A 203 -111.00 -83.32 REMARK 500 LEU A 204 113.96 61.53 REMARK 500 GLN A 298 -157.80 -72.28 REMARK 500 SER A 299 2.50 55.96 REMARK 500 LEU A 303 3.54 -66.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NAC RELATED DB: PDB DBREF 4NAD B 177 326 UNP Q9NQG5 RPR1B_HUMAN 177 326 DBREF 4NAD A 177 326 UNP Q9NQG5 RPR1B_HUMAN 177 326 SEQADV 4NAD ALA B 173 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD MET B 174 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD GLY B 175 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD SER B 176 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD ALA A 173 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD MET A 174 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD GLY A 175 UNP Q9NQG5 EXPRESSION TAG SEQADV 4NAD SER A 176 UNP Q9NQG5 EXPRESSION TAG SEQRES 1 B 154 ALA MET GLY SER THR GLU GLU LEU ILE LYS ALA LEU GLN SEQRES 2 B 154 ASP LEU GLU ASN ALA ALA SER GLY ASP ALA THR VAL ARG SEQRES 3 B 154 GLN LYS ILE ALA SER LEU PRO GLN GLU VAL GLN ASP VAL SEQRES 4 B 154 SER LEU LEU GLU LYS ILE THR ASP LYS GLU ALA ALA GLU SEQRES 5 B 154 ARG LEU SER LYS THR VAL ASP GLU ALA CYS LEU LEU LEU SEQRES 6 B 154 ALA GLU TYR ASN GLY ARG LEU ALA ALA GLU LEU GLU ASP SEQRES 7 B 154 ARG ARG GLN LEU ALA ARG MET LEU VAL GLU TYR THR GLN SEQRES 8 B 154 ASN GLN LYS ASP VAL LEU SER GLU LYS GLU LYS LYS LEU SEQRES 9 B 154 GLU GLU TYR LYS GLN LYS LEU ALA ARG VAL THR GLN VAL SEQRES 10 B 154 ARG LYS GLU LEU LYS SER HIS ILE GLN SER LEU PRO ASP SEQRES 11 B 154 LEU SER LEU LEU PRO ASN VAL THR GLY GLY LEU ALA PRO SEQRES 12 B 154 LEU PRO SER ALA GLY ASP LEU PHE SER THR ASP SEQRES 1 A 154 ALA MET GLY SER THR GLU GLU LEU ILE LYS ALA LEU GLN SEQRES 2 A 154 ASP LEU GLU ASN ALA ALA SER GLY ASP ALA THR VAL ARG SEQRES 3 A 154 GLN LYS ILE ALA SER LEU PRO GLN GLU VAL GLN ASP VAL SEQRES 4 A 154 SER LEU LEU GLU LYS ILE THR ASP LYS GLU ALA ALA GLU SEQRES 5 A 154 ARG LEU SER LYS THR VAL ASP GLU ALA CYS LEU LEU LEU SEQRES 6 A 154 ALA GLU TYR ASN GLY ARG LEU ALA ALA GLU LEU GLU ASP SEQRES 7 A 154 ARG ARG GLN LEU ALA ARG MET LEU VAL GLU TYR THR GLN SEQRES 8 A 154 ASN GLN LYS ASP VAL LEU SER GLU LYS GLU LYS LYS LEU SEQRES 9 A 154 GLU GLU TYR LYS GLN LYS LEU ALA ARG VAL THR GLN VAL SEQRES 10 A 154 ARG LYS GLU LEU LYS SER HIS ILE GLN SER LEU PRO ASP SEQRES 11 A 154 LEU SER LEU LEU PRO ASN VAL THR GLY GLY LEU ALA PRO SEQRES 12 A 154 LEU PRO SER ALA GLY ASP LEU PHE SER THR ASP HELIX 1 1 SER B 176 ASP B 186 1 11 HELIX 2 2 LEU B 187 ALA B 191 5 5 HELIX 3 3 GLY B 193 SER B 203 1 11 HELIX 4 4 PRO B 205 GLN B 209 5 5 HELIX 5 5 ASP B 210 ILE B 217 5 8 HELIX 6 6 ASP B 219 GLN B 298 1 80 HELIX 7 7 SER A 176 ASP A 186 1 11 HELIX 8 8 LEU A 187 ALA A 191 5 5 HELIX 9 9 GLY A 193 SER A 203 1 11 HELIX 10 10 PRO A 205 GLN A 209 5 5 HELIX 11 11 ASP A 210 ILE A 217 5 8 HELIX 12 12 ASP A 219 GLN A 298 1 80 CISPEP 1 MET B 174 GLY B 175 0 -8.25 CISPEP 2 GLY B 175 SER B 176 0 0.50 CISPEP 3 MET A 174 GLY A 175 0 -1.42 CRYST1 33.280 55.660 84.450 90.00 92.90 90.00 P 1 21 1 4 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 0.030048 0.000000 0.001522 0.00000 SCALE2 0.000000 0.017966 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011856 0.00000