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
(ATOM LINES ARE NOT SHOWN.)
END