HEADER CELL CYCLE 30-NOV-23 8R99 TITLE A SOAKABLE CRYSTAL FORM OF HUMAN CDK7 IN COMPLEX WITH AMP-PNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE 7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDK7; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 9 KEYWDS SERINE-THREONINE KINASE, PHOSPHORYLATION, CELL CYCLE PROGRESSION, ATP KEYWDS 2 BINDING, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR M.MUKHERJEE,A.CLEASBY REVDAT 2 26-JUN-24 8R99 1 JRNL REVDAT 1 29-MAY-24 8R99 0 JRNL AUTH M.MUKHERJEE,P.J.DAY,D.LAVERTY,J.A.BUEREN-CALABUIG, JRNL AUTH 2 A.J.WOODHEAD,C.GRIFFITHS-JONES,S.HISCOCK,C.EAST,S.BOYD, JRNL AUTH 3 M.O'REILLY JRNL TITL PROTEIN ENGINEERING ENABLES A SOAKABLE CRYSTAL FORM OF HUMAN JRNL TITL 2 CDK7 PRIMED FOR HIGH-THROUGHPUT CRYSTALLOGRAPHY AND JRNL TITL 3 STRUCTURE-BASED DRUG DESIGN. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38870939 JRNL DOI 10.1016/J.STR.2024.05.011 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 64.7 REMARK 3 NUMBER OF REFLECTIONS : 23054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1249 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 115 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 4.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 6 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : -0.22000 REMARK 3 B33 (A**2) : -0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.166 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.155 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.108 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.235 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2379 ; 0.009 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2183 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3235 ; 1.393 ; 1.783 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5113 ; 0.477 ; 1.729 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 296 ;16.708 ; 5.456 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;31.704 ;21.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 388 ;16.952 ;15.052 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;21.723 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 306 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2615 ; 0.001 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 436 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1148 ; 3.105 ; 5.852 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1149 ; 3.105 ; 5.859 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1231 ; 4.265 ; 7.176 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1232 ; 4.266 ; 7.178 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2603 ; 9.448 ;32.463 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2589 ; 9.418 ;32.275 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 95 REMARK 3 ORIGIN FOR THE GROUP (A): -17.1803 6.1166 14.5211 REMARK 3 T TENSOR REMARK 3 T11: 0.4541 T22: 0.5034 REMARK 3 T33: 0.3920 T12: -0.0135 REMARK 3 T13: -0.1635 T23: -0.0446 REMARK 3 L TENSOR REMARK 3 L11: 4.9727 L22: 6.9681 REMARK 3 L33: 5.9145 L12: 1.1997 REMARK 3 L13: 2.7170 L23: 0.1839 REMARK 3 S TENSOR REMARK 3 S11: -0.0384 S12: -0.8676 S13: 0.2691 REMARK 3 S21: 1.4930 S22: -0.1804 S23: -1.2038 REMARK 3 S31: -0.2629 S32: 0.7655 S33: 0.2188 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 96 A 311 REMARK 3 ORIGIN FOR THE GROUP (A): -19.4665 -0.8144 -10.8018 REMARK 3 T TENSOR REMARK 3 T11: 0.0103 T22: 0.0373 REMARK 3 T33: 0.0668 T12: 0.0025 REMARK 3 T13: -0.0156 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 3.5885 L22: 1.7979 REMARK 3 L33: 2.4578 L12: 0.1438 REMARK 3 L13: -1.7302 L23: -0.1436 REMARK 3 S TENSOR REMARK 3 S11: -0.0050 S12: 0.2550 S13: 0.0912 REMARK 3 S21: -0.0936 S22: -0.0133 S23: -0.0527 REMARK 3 S31: -0.0163 S32: 0.0387 S33: 0.0183 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8R99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1292134977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24282 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.809 REMARK 200 RESOLUTION RANGE LOW (A) : 72.436 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 5.620 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: .1M (NH4)3 CITRATE .2M NDSB-201 15.2% REMARK 280 PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 72.43600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.11600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 72.43600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.11600 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: 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 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 -24 REMARK 465 SER A -23 REMARK 465 TYR A -22 REMARK 465 TYR A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 ASP A -14 REMARK 465 TYR A -13 REMARK 465 ASP A -12 REMARK 465 ILE A -11 REMARK 465 PRO A -10 REMARK 465 THR A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 VAL A 5 REMARK 465 LYS A 6 REMARK 465 SER A 7 REMARK 465 ARG A 8 REMARK 465 ALA A 9 REMARK 465 GLU A 20 REMARK 465 GLY A 21 REMARK 465 GLN A 22 REMARK 465 PHE A 23 REMARK 465 LYS A 44 REMARK 465 LEU A 45 REMARK 465 GLY A 46 REMARK 465 HIS A 47 REMARK 465 ARG A 48 REMARK 465 SER A 49 REMARK 465 GLU A 50 REMARK 465 ALA A 51 REMARK 465 LYS A 52 REMARK 465 ASP A 53 REMARK 465 GLY A 54 REMARK 465 ILE A 55 REMARK 465 ASN A 56 REMARK 465 HIS A 83 REMARK 465 LYS A 84 REMARK 465 CYS A 312 REMARK 465 PRO A 313 REMARK 465 VAL A 314 REMARK 465 GLU A 315 REMARK 465 THR A 316 REMARK 465 LEU A 317 REMARK 465 LYS A 318 REMARK 465 GLU A 319 REMARK 465 GLN A 320 REMARK 465 SER A 321 REMARK 465 ASN A 322 REMARK 465 PRO A 323 REMARK 465 ALA A 324 REMARK 465 LEU A 325 REMARK 465 ALA A 326 REMARK 465 ILE A 327 REMARK 465 LYS A 328 REMARK 465 ARG A 329 REMARK 465 LYS A 330 REMARK 465 ARG A 331 REMARK 465 THR A 332 REMARK 465 GLU A 333 REMARK 465 ALA A 334 REMARK 465 LEU A 335 REMARK 465 GLU A 336 REMARK 465 GLN A 337 REMARK 465 GLY A 338 REMARK 465 GLY A 339 REMARK 465 LEU A 340 REMARK 465 PRO A 341 REMARK 465 LYS A 342 REMARK 465 LYS A 343 REMARK 465 LEU A 344 REMARK 465 ILE A 345 REMARK 465 PHE A 346 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 ARG A 179 NE - CZ - NH2 ANGL. DEV. = 3.4 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 LEU A 15 -127.33 -81.40 REMARK 500 ASN A 33 -74.62 -70.44 REMARK 500 ASP A 137 44.35 -144.06 REMARK 500 ASP A 155 80.05 62.42 REMARK 500 PHE A 156 32.41 -92.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 309 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 142 OD1 REMARK 620 2 ANP A 401 O2G 136.8 REMARK 620 3 ANP A 401 O1B 136.2 73.0 REMARK 620 N 1 2 DBREF 8R99 A 1 346 UNP P50613 CDK7_HUMAN 1 346 SEQADV 8R99 MET A -24 UNP P50613 INITIATING METHIONINE SEQADV 8R99 SER A -23 UNP P50613 EXPRESSION TAG SEQADV 8R99 TYR A -22 UNP P50613 EXPRESSION TAG SEQADV 8R99 TYR A -21 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -20 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -19 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -18 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -17 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -16 UNP P50613 EXPRESSION TAG SEQADV 8R99 HIS A -15 UNP P50613 EXPRESSION TAG SEQADV 8R99 ASP A -14 UNP P50613 EXPRESSION TAG SEQADV 8R99 TYR A -13 UNP P50613 EXPRESSION TAG SEQADV 8R99 ASP A -12 UNP P50613 EXPRESSION TAG SEQADV 8R99 ILE A -11 UNP P50613 EXPRESSION TAG SEQADV 8R99 PRO A -10 UNP P50613 EXPRESSION TAG SEQADV 8R99 THR A -9 UNP P50613 EXPRESSION TAG SEQADV 8R99 THR A -8 UNP P50613 EXPRESSION TAG SEQADV 8R99 GLU A -7 UNP P50613 EXPRESSION TAG SEQADV 8R99 ASN A -6 UNP P50613 EXPRESSION TAG SEQADV 8R99 LEU A -5 UNP P50613 EXPRESSION TAG SEQADV 8R99 TYR A -4 UNP P50613 EXPRESSION TAG SEQADV 8R99 PHE A -3 UNP P50613 EXPRESSION TAG SEQADV 8R99 GLN A -2 UNP P50613 EXPRESSION TAG SEQADV 8R99 GLY A -1 UNP P50613 EXPRESSION TAG SEQADV 8R99 SER A 0 UNP P50613 EXPRESSION TAG SEQADV 8R99 ARG A 132 UNP P50613 TRP 132 ENGINEERED MUTATION SEQADV 8R99 ASP A 164 UNP P50613 SER 164 ENGINEERED MUTATION SEQADV 8R99 GLU A 170 UNP P50613 THR 170 ENGINEERED MUTATION SEQRES 1 A 371 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 371 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY SER MET SEQRES 3 A 371 ALA LEU ASP VAL LYS SER ARG ALA LYS ARG TYR GLU LYS SEQRES 4 A 371 LEU ASP PHE LEU GLY GLU GLY GLN PHE ALA THR VAL TYR SEQRES 5 A 371 LYS ALA ARG ASP LYS ASN THR ASN GLN ILE VAL ALA ILE SEQRES 6 A 371 LYS LYS ILE LYS LEU GLY HIS ARG SER GLU ALA LYS ASP SEQRES 7 A 371 GLY ILE ASN ARG THR ALA LEU ARG GLU ILE LYS LEU LEU SEQRES 8 A 371 GLN GLU LEU SER HIS PRO ASN ILE ILE GLY LEU LEU ASP SEQRES 9 A 371 ALA PHE GLY HIS LYS SER ASN ILE SER LEU VAL PHE ASP SEQRES 10 A 371 PHE MET GLU THR ASP LEU GLU VAL ILE ILE LYS ASP ASN SEQRES 11 A 371 SER LEU VAL LEU THR PRO SER HIS ILE LYS ALA TYR MET SEQRES 12 A 371 LEU MET THR LEU GLN GLY LEU GLU TYR LEU HIS GLN HIS SEQRES 13 A 371 ARG ILE LEU HIS ARG ASP LEU LYS PRO ASN ASN LEU LEU SEQRES 14 A 371 LEU ASP GLU ASN GLY VAL LEU LYS LEU ALA ASP PHE GLY SEQRES 15 A 371 LEU ALA LYS SER PHE GLY ASP PRO ASN ARG ALA TYR GLU SEQRES 16 A 371 HIS GLN VAL VAL THR ARG TRP TYR ARG ALA PRO GLU LEU SEQRES 17 A 371 LEU PHE GLY ALA ARG MET TYR GLY VAL GLY VAL ASP MET SEQRES 18 A 371 TRP ALA VAL GLY CYS ILE LEU ALA GLU LEU LEU LEU ARG SEQRES 19 A 371 VAL PRO PHE LEU PRO GLY ASP SER ASP LEU ASP GLN LEU SEQRES 20 A 371 THR ARG ILE PHE GLU THR LEU GLY THR PRO THR GLU GLU SEQRES 21 A 371 GLN TRP PRO ASP MET CYS SER LEU PRO ASP TYR VAL THR SEQRES 22 A 371 PHE LYS SER PHE PRO GLY ILE PRO LEU HIS HIS ILE PHE SEQRES 23 A 371 SER ALA ALA GLY ASP ASP LEU LEU ASP LEU ILE GLN GLY SEQRES 24 A 371 LEU PHE LEU PHE ASN PRO CYS ALA ARG ILE THR ALA THR SEQRES 25 A 371 GLN ALA LEU LYS MET LYS TYR PHE SER ASN ARG PRO GLY SEQRES 26 A 371 PRO THR PRO GLY CYS GLN LEU PRO ARG PRO ASN CYS PRO SEQRES 27 A 371 VAL GLU THR LEU LYS GLU GLN SER ASN PRO ALA LEU ALA SEQRES 28 A 371 ILE LYS ARG LYS ARG THR GLU ALA LEU GLU GLN GLY GLY SEQRES 29 A 371 LEU PRO LYS LYS LEU ILE PHE HET ANP A 401 44 HET MG A 402 1 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 2 ANP C10 H17 N6 O12 P3 FORMUL 3 MG MG 2+ FORMUL 4 HOH *222(H2 O) HELIX 1 AA1 THR A 58 LEU A 69 1 12 HELIX 2 AA2 LEU A 98 ASP A 104 1 7 HELIX 3 AA3 THR A 110 HIS A 131 1 22 HELIX 4 AA4 LYS A 139 ASN A 141 5 3 HELIX 5 AA5 THR A 175 ARG A 179 5 5 HELIX 6 AA6 ALA A 180 PHE A 185 1 6 HELIX 7 AA7 VAL A 192 ARG A 209 1 18 HELIX 8 AA8 SER A 217 GLY A 230 1 14 HELIX 9 AA9 TRP A 237 LEU A 243 5 7 HELIX 10 AB1 PRO A 256 PHE A 261 1 6 HELIX 11 AB2 GLY A 265 PHE A 276 1 12 HELIX 12 AB3 THR A 285 MET A 292 1 8 HELIX 13 AB4 MET A 292 ASN A 297 1 6 HELIX 14 AB5 PRO A 303 LEU A 307 5 5 SHEET 1 AA1 5 TYR A 12 PHE A 17 0 SHEET 2 AA1 5 THR A 25 ASP A 31 -1 O LYS A 28 N ASP A 16 SHEET 3 AA1 5 ILE A 37 LYS A 42 -1 O ILE A 40 N TYR A 27 SHEET 4 AA1 5 SER A 88 ASP A 92 -1 O PHE A 91 N ALA A 39 SHEET 5 AA1 5 LEU A 77 PHE A 81 -1 N ASP A 79 O VAL A 90 SHEET 1 AA2 3 THR A 96 ASP A 97 0 SHEET 2 AA2 3 LEU A 143 LEU A 145 -1 O LEU A 145 N THR A 96 SHEET 3 AA2 3 LEU A 151 LEU A 153 -1 O LYS A 152 N LEU A 144 SHEET 1 AA3 2 ILE A 133 LEU A 134 0 SHEET 2 AA3 2 LYS A 160 SER A 161 -1 O LYS A 160 N LEU A 134 LINK OD1 ASN A 142 MG MG A 402 1555 1555 2.36 LINK O2G ANP A 401 MG MG A 402 1555 1555 2.54 LINK O1B ANP A 401 MG MG A 402 1555 1555 2.73 CISPEP 1 ARG A 298 PRO A 299 0 -2.78 CRYST1 144.872 40.232 68.589 90.00 90.00 90.00 P 21 21 2 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 0.006903 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014580 0.00000