HEADER TRANSCRIPTION 22-OCT-13 4NAC TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF P15RS COMPND MOL_ID: 1; COMPND 2 MOLECULE: REGULATION OF NUCLEAR PRE-MRNA DOMAIN-CONTAINING PROTEIN COMPND 3 1A; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 1-131; COMPND 6 SYNONYM: CYCLIN-DEPENDENT KINASE INHIBITOR 2B-RELATED PROTEIN, COMPND 7 P15INK4B-RELATED PROTEIN; COMPND 8 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: P15RS, RPRD1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ALPHA HELIX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.MEI,Z.JIN,F.REN,Y.WANG REVDAT 3 20-MAR-24 4NAC 1 SEQADV REVDAT 2 15-NOV-17 4NAC 1 REMARK REVDAT 1 11-DEC-13 4NAC 0 JRNL AUTH K.MEI,Z.JIN,F.REN,Y.WANG,Z.CHANG,X.WANG JRNL TITL CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF P15RS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_596 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 18187 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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 30.3330 - 3.8265 0.99 2564 150 0.1723 0.1951 REMARK 3 2 3.8265 - 3.0381 0.99 2532 137 0.1626 0.1930 REMARK 3 3 3.0381 - 2.6544 0.99 2499 112 0.1883 0.2242 REMARK 3 4 2.6544 - 2.4118 0.98 2481 138 0.1757 0.2344 REMARK 3 5 2.4118 - 2.2390 0.97 2433 142 0.1632 0.2336 REMARK 3 6 2.2390 - 2.1070 0.96 2416 120 0.1718 0.2169 REMARK 3 7 2.1070 - 2.0015 0.94 2332 131 0.2004 0.2735 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 43.48 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08110 REMARK 3 B22 (A**2) : -2.58090 REMARK 3 B33 (A**2) : 1.49980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.38750 REMARK 3 B23 (A**2) : 0.00000 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 : 0.007 2256 REMARK 3 ANGLE : 0.908 3041 REMARK 3 CHIRALITY : 0.061 333 REMARK 3 PLANARITY : 0.004 384 REMARK 3 DIHEDRAL : 14.690 851 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: NULL REMARK 4 REMARK 4 4NAC 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_1000082951. 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 : 7.0 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) : 0.98000 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 : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18187 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.002 REMARK 200 RESOLUTION RANGE LOW (A) : 30.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 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 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: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M DL-MALIC ACID, 0.1M BIS-TRIS REMARK 280 PROPANE, PH 7.0, VAPOR DIFFUSION, 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 23.66300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 SER A 2 REMARK 465 ALA A 3 REMARK 465 MET B 1 REMARK 465 GLU B 133 REMARK 465 HIS B 134 REMARK 465 HIS B 135 REMARK 465 HIS B 136 REMARK 465 HIS B 137 REMARK 465 HIS B 138 REMARK 465 HIS B 139 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 SG CYS A 100 O HOH A 287 1.90 REMARK 500 O HOH A 227 O HOH A 248 1.95 REMARK 500 N PHE A 4 O HOH A 288 2.01 REMARK 500 O HOH A 207 O HOH A 236 2.08 REMARK 500 O HOH A 305 O HOH A 322 2.08 REMARK 500 O HOH A 247 O HOH A 319 2.09 REMARK 500 O HOH A 270 O HOH A 319 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C HIS A 139 O HOH B 211 2547 2.07 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 HIS A 33 31.66 -96.58 REMARK 500 HIS B 33 32.48 -96.52 REMARK 500 GLU B 95 44.16 -85.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NAD RELATED DB: PDB DBREF 4NAC A 1 131 UNP Q96P16 RPR1A_HUMAN 1 131 DBREF 4NAC B 1 131 UNP Q96P16 RPR1A_HUMAN 1 131 SEQADV 4NAC LEU A 132 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC GLU A 133 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 134 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 135 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 136 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 137 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 138 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS A 139 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC LEU B 132 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC GLU B 133 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 134 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 135 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 136 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 137 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 138 UNP Q96P16 EXPRESSION TAG SEQADV 4NAC HIS B 139 UNP Q96P16 EXPRESSION TAG SEQRES 1 A 139 MET SER ALA PHE SER GLU ALA ALA LEU GLU LYS LYS LEU SEQRES 2 A 139 SER GLU LEU SER ASN SER GLN GLN SER VAL GLN THR LEU SEQRES 3 A 139 SER LEU TRP LEU ILE HIS HIS ARG LYS HIS SER ARG PRO SEQRES 4 A 139 ILE VAL THR VAL TRP GLU ARG GLU LEU ARG LYS ALA LYS SEQRES 5 A 139 PRO ASN ARG LYS LEU THR PHE LEU TYR LEU ALA ASN ASP SEQRES 6 A 139 VAL ILE GLN ASN SER LYS ARG LYS GLY PRO GLU PHE THR SEQRES 7 A 139 LYS ASP PHE ALA PRO VAL ILE VAL GLU ALA PHE LYS HIS SEQRES 8 A 139 VAL SER SER GLU THR ASP GLU SER CYS LYS LYS HIS LEU SEQRES 9 A 139 GLY ARG VAL LEU SER ILE TRP GLU GLU ARG SER VAL TYR SEQRES 10 A 139 GLU ASN ASP VAL LEU GLU GLN LEU LYS GLN ALA LEU TYR SEQRES 11 A 139 GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 139 MET SER ALA PHE SER GLU ALA ALA LEU GLU LYS LYS LEU SEQRES 2 B 139 SER GLU LEU SER ASN SER GLN GLN SER VAL GLN THR LEU SEQRES 3 B 139 SER LEU TRP LEU ILE HIS HIS ARG LYS HIS SER ARG PRO SEQRES 4 B 139 ILE VAL THR VAL TRP GLU ARG GLU LEU ARG LYS ALA LYS SEQRES 5 B 139 PRO ASN ARG LYS LEU THR PHE LEU TYR LEU ALA ASN ASP SEQRES 6 B 139 VAL ILE GLN ASN SER LYS ARG LYS GLY PRO GLU PHE THR SEQRES 7 B 139 LYS ASP PHE ALA PRO VAL ILE VAL GLU ALA PHE LYS HIS SEQRES 8 B 139 VAL SER SER GLU THR ASP GLU SER CYS LYS LYS HIS LEU SEQRES 9 B 139 GLY ARG VAL LEU SER ILE TRP GLU GLU ARG SER VAL TYR SEQRES 10 B 139 GLU ASN ASP VAL LEU GLU GLN LEU LYS GLN ALA LEU TYR SEQRES 11 B 139 GLY LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *221(H2 O) HELIX 1 1 SER A 5 GLU A 15 1 11 HELIX 2 2 SER A 19 HIS A 33 1 15 HELIX 3 3 HIS A 36 ALA A 51 1 16 HELIX 4 4 LYS A 52 LYS A 71 1 20 HELIX 5 5 PRO A 75 THR A 96 1 22 HELIX 6 6 ASP A 97 SER A 99 5 3 HELIX 7 7 CYS A 100 ARG A 114 1 15 HELIX 8 8 GLU A 118 GLY A 131 1 14 HELIX 9 9 LEU A 132 HIS A 136 5 5 HELIX 10 10 SER B 5 LEU B 16 1 12 HELIX 11 11 SER B 19 HIS B 33 1 15 HELIX 12 12 HIS B 36 ALA B 51 1 16 HELIX 13 13 LYS B 52 LYS B 71 1 20 HELIX 14 14 PRO B 75 GLU B 95 1 21 HELIX 15 15 ASP B 97 ARG B 114 1 18 HELIX 16 16 GLU B 118 GLY B 131 1 14 CRYST1 43.691 47.326 68.019 90.00 100.24 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 0.022888 0.000000 0.004134 0.00000 SCALE2 0.000000 0.021130 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014940 0.00000