PDB Short entry for 4BGQ HEADER TRANSFERASE 28-MAR-13 4BGQ TITLE CRYSTAL STRUCTURE OF THE HUMAN CDKL5 KINASE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIN-DEPENDENT KINASE-LIKE 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, RESIDUES 1-303; COMPND 5 SYNONYM: SERINE/THREONINE-PROTEIN KINASE 9; COMPND 6 EC: 2.7.11.22; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE; SOURCE 11 OTHER_DETAILS: SITE-DIRECTED MUTAGENESIS KEYWDS TRANSFERASE, PHOSPHO-MIMETIC, KINASE EXPDTA X-RAY DIFFRACTION AUTHOR P.CANNING,T.KROJER,S.GOUBIN,P.MAHAJAN,M.VOLLMAR,A.C.W.PIKE,F.VON AUTHOR 2 DELFT,C.H.ARROWSMITH,A.M.EDWARDS,C.BOUNTRA,A.BULLOCK REVDAT 4 20-DEC-23 4BGQ 1 REMARK REVDAT 3 30-MAR-22 4BGQ 1 JRNL REMARK REVDAT 2 24-JAN-18 4BGQ 1 JRNL REVDAT 1 08-MAY-13 4BGQ 0 JRNL AUTH P.CANNING,K.PARK,J.GONCALVES,C.LI,C.J.HOWARD,T.D.SHARPE, JRNL AUTH 2 L.J.HOLT,L.PELLETIER,A.N.BULLOCK,M.R.LEROUX JRNL TITL CDKL FAMILY KINASES HAVE EVOLVED DISTINCT STRUCTURAL JRNL TITL 2 FEATURES AND CILIARY FUNCTION. JRNL REF CELL REP V. 22 885 2018 JRNL REFN ESSN 2211-1247 JRNL PMID 29420175 JRNL DOI 10.1016/J.CELREP.2017.12.083 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23136 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1243 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1660 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 152 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -14.70000 REMARK 3 B22 (A**2) : 4.05000 REMARK 3 B33 (A**2) : 10.65000 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): 0.032 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.028 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.306 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2313 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2252 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3129 ; 1.290 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5170 ; 0.788 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 281 ; 5.818 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 100 ;33.526 ;23.900 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 405 ;13.146 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;24.315 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 347 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2559 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 527 ; 0.001 ; 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): 1111 ; 1.631 ; 2.391 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1108 ; 1.615 ; 2.386 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1383 ; 2.713 ; 3.557 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1202 ; 1.881 ; 2.606 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 8 A 47 REMARK 3 ORIGIN FOR THE GROUP (A): 58.0346 30.4809 48.0009 REMARK 3 T TENSOR REMARK 3 T11: 0.0715 T22: 0.0762 REMARK 3 T33: 0.0821 T12: -0.0182 REMARK 3 T13: 0.0008 T23: -0.0586 REMARK 3 L TENSOR REMARK 3 L11: 1.8472 L22: 4.8537 REMARK 3 L33: 1.5186 L12: -2.9578 REMARK 3 L13: -0.4984 L23: 1.1553 REMARK 3 S TENSOR REMARK 3 S11: -0.1341 S12: -0.1220 S13: 0.3308 REMARK 3 S21: 0.1414 S22: 0.2152 S23: -0.5528 REMARK 3 S31: -0.1696 S32: -0.0605 S33: -0.0812 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 52 A 162 REMARK 3 ORIGIN FOR THE GROUP (A): 47.3400 26.7840 61.8775 REMARK 3 T TENSOR REMARK 3 T11: 0.0150 T22: 0.0212 REMARK 3 T33: 0.0165 T12: 0.0010 REMARK 3 T13: 0.0102 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.1191 L22: 0.0274 REMARK 3 L33: 0.2420 L12: -0.1657 REMARK 3 L13: -0.5094 L23: 0.0700 REMARK 3 S TENSOR REMARK 3 S11: -0.0100 S12: 0.0078 S13: -0.0227 REMARK 3 S21: -0.0046 S22: -0.0052 S23: -0.0016 REMARK 3 S31: 0.0126 S32: -0.0012 S33: 0.0152 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 163 A 237 REMARK 3 ORIGIN FOR THE GROUP (A): 33.5234 38.6380 71.7383 REMARK 3 T TENSOR REMARK 3 T11: 0.0238 T22: 0.0404 REMARK 3 T33: 0.0157 T12: 0.0022 REMARK 3 T13: 0.0123 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.2595 L22: 0.8479 REMARK 3 L33: 0.5167 L12: -0.2123 REMARK 3 L13: -0.0580 L23: 0.6235 REMARK 3 S TENSOR REMARK 3 S11: 0.0151 S12: 0.0120 S13: 0.0336 REMARK 3 S21: -0.0264 S22: 0.0442 S23: -0.0870 REMARK 3 S31: -0.0229 S32: 0.0224 S33: -0.0593 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 238 A 302 REMARK 3 ORIGIN FOR THE GROUP (A): 27.7949 32.3378 72.3032 REMARK 3 T TENSOR REMARK 3 T11: 0.0094 T22: 0.0275 REMARK 3 T33: 0.0273 T12: -0.0055 REMARK 3 T13: 0.0053 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 0.1908 L22: 0.5629 REMARK 3 L33: 0.2997 L12: -0.1611 REMARK 3 L13: -0.0024 L23: 0.2993 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: -0.0519 S13: -0.0120 REMARK 3 S21: 0.0150 S22: 0.0195 S23: -0.0058 REMARK 3 S31: 0.0287 S32: -0.0476 S33: -0.0033 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. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 4BGQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1290056324. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-13 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23993 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 55.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.6000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.800 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: PDB ENTRY 4BBM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG SMEAR MEDIUM, 0.1M TRIS PH REMARK 280 8.0, 0.075M SODIUM ACETATE, 0.15M SODIUM CHLORIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 25.97100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.44950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.75350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.44950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.97100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.75350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 0 REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ILE A 3 REMARK 465 PRO A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 ASN A 8 REMARK 465 ASP A 46 REMARK 465 SER A 47 REMARK 465 GLU A 48 REMARK 465 GLU A 49 REMARK 465 ASN A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 52 REMARK 465 GLY A 163 REMARK 465 ASN A 164 REMARK 465 ASN A 165 REMARK 465 ALA A 166 REMARK 465 ASN A 167 REMARK 465 TYR A 168 REMARK 465 ASP A 169 REMARK 465 GLU A 170 REMARK 465 GLU A 171 REMARK 465 VAL A 172 REMARK 465 ALA A 173 REMARK 465 LEU A 303 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 VAL A 9 CG1 CG2 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 GLU A 21 CG CD OE1 OE2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 LYS A 54 CE NZ REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 ARG A 81 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 LYS A 113 CD CE NZ REMARK 470 THR A 174 OG1 CG2 REMARK 470 ARG A 178 NE CZ NH1 NH2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 LEU A 302 CG CD1 CD2 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 O HOH A 2051 O HOH A 2115 1.93 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 ARG A 134 -5.16 74.93 REMARK 500 ASP A 135 39.89 -142.31 REMARK 500 ASP A 153 66.75 68.85 REMARK 500 ASN A 253 -83.67 -90.44 REMARK 500 SER A 257 143.53 82.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 38R A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1005 REMARK 999 REMARK 999 SEQUENCE REMARK 999 TWO PHOSPHOMIMETIC MUTATIONS INTRODUCED, T169D AND Y171E DBREF 4BGQ A 1 303 UNP O76039 CDKL5_HUMAN 1 303 SEQADV 4BGQ SER A 0 UNP O76039 EXPRESSION TAG SEQADV 4BGQ ASP A 169 UNP O76039 THR 169 ENGINEERED MUTATION SEQADV 4BGQ GLU A 171 UNP O76039 TYR 171 ENGINEERED MUTATION SEQRES 1 A 304 SER MET LYS ILE PRO ASN ILE GLY ASN VAL MET ASN LYS SEQRES 2 A 304 PHE GLU ILE LEU GLY VAL VAL GLY GLU GLY ALA TYR GLY SEQRES 3 A 304 VAL VAL LEU LYS CYS ARG HIS LYS GLU THR HIS GLU ILE SEQRES 4 A 304 VAL ALA ILE LYS LYS PHE LYS ASP SER GLU GLU ASN GLU SEQRES 5 A 304 GLU VAL LYS GLU THR THR LEU ARG GLU LEU LYS MET LEU SEQRES 6 A 304 ARG THR LEU LYS GLN GLU ASN ILE VAL GLU LEU LYS GLU SEQRES 7 A 304 ALA PHE ARG ARG ARG GLY LYS LEU TYR LEU VAL PHE GLU SEQRES 8 A 304 TYR VAL GLU LYS ASN MET LEU GLU LEU LEU GLU GLU MET SEQRES 9 A 304 PRO ASN GLY VAL PRO PRO GLU LYS VAL LYS SER TYR ILE SEQRES 10 A 304 TYR GLN LEU ILE LYS ALA ILE HIS TRP CYS HIS LYS ASN SEQRES 11 A 304 ASP ILE VAL HIS ARG ASP ILE LYS PRO GLU ASN LEU LEU SEQRES 12 A 304 ILE SER HIS ASN ASP VAL LEU LYS LEU CYS ASP PHE GLY SEQRES 13 A 304 PHE ALA ARG ASN LEU SER GLU GLY ASN ASN ALA ASN TYR SEQRES 14 A 304 ASP GLU GLU VAL ALA THR ARG TRP TYR ARG SER PRO GLU SEQRES 15 A 304 LEU LEU LEU GLY ALA PRO TYR GLY LYS SER VAL ASP MET SEQRES 16 A 304 TRP SER VAL GLY CYS ILE LEU GLY GLU LEU SER ASP GLY SEQRES 17 A 304 GLN PRO LEU PHE PRO GLY GLU SER GLU ILE ASP GLN LEU SEQRES 18 A 304 PHE THR ILE GLN LYS VAL LEU GLY PRO LEU PRO SER GLU SEQRES 19 A 304 GLN MET LYS LEU PHE TYR SER ASN PRO ARG PHE HIS GLY SEQRES 20 A 304 LEU ARG PHE PRO ALA VAL ASN HIS PRO GLN SER LEU GLU SEQRES 21 A 304 ARG ARG TYR LEU GLY ILE LEU ASN SER VAL LEU LEU ASP SEQRES 22 A 304 LEU MET LYS ASN LEU LEU LYS LEU ASP PRO ALA ASP ARG SEQRES 23 A 304 TYR LEU THR GLU GLN CYS LEU ASN HIS PRO THR PHE GLN SEQRES 24 A 304 THR GLN ARG LEU LEU HET NA A1003 1 HET 38R A1000 27 HET EDO A1001 4 HET ACT A1002 4 HET ACT A1004 4 HET EDO A1005 4 HETNAM NA SODIUM ION HETNAM 38R [4-({4-[(3-CYCLOPENTYL-1H-PYRAZOL-5-YL)AMINO]PYRIMIDIN- HETNAM 2 38R 2-YL}AMINO)PHENYL]ACETONITRILE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NA NA 1+ FORMUL 3 38R C20 H21 N7 FORMUL 4 EDO 2(C2 H6 O2) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 8 HOH *152(H2 O) HELIX 1 1 LYS A 54 LEU A 67 1 14 HELIX 2 2 MET A 96 MET A 103 1 8 HELIX 3 3 PRO A 108 ASN A 129 1 22 HELIX 4 4 LYS A 137 GLU A 139 5 3 HELIX 5 5 SER A 179 LEU A 184 1 6 HELIX 6 6 LYS A 190 GLY A 207 1 18 HELIX 7 7 SER A 215 GLY A 228 1 14 HELIX 8 8 PRO A 231 ASN A 241 1 11 HELIX 9 9 PRO A 242 HIS A 245 5 4 HELIX 10 10 SER A 257 LEU A 263 1 7 HELIX 11 11 ASN A 267 LEU A 278 1 12 HELIX 12 12 ASP A 281 ARG A 285 5 5 HELIX 13 13 LEU A 287 ASN A 293 1 7 HELIX 14 14 HIS A 294 THR A 299 1 6 SHEET 1 AA 5 PHE A 13 GLU A 21 0 SHEET 2 AA 5 VAL A 26 HIS A 32 -1 O VAL A 27 N VAL A 19 SHEET 3 AA 5 ILE A 38 LYS A 43 -1 O VAL A 39 N CYS A 30 SHEET 4 AA 5 LYS A 84 GLU A 90 -1 O LEU A 87 N LYS A 42 SHEET 5 AA 5 LEU A 75 ARG A 81 -1 N LYS A 76 O VAL A 88 SHEET 1 AB 3 LYS A 94 ASN A 95 0 SHEET 2 AB 3 LEU A 141 ILE A 143 -1 O ILE A 143 N LYS A 94 SHEET 3 AB 3 LEU A 149 LEU A 151 -1 O LYS A 150 N LEU A 142 SHEET 1 AC 2 ILE A 131 VAL A 132 0 SHEET 2 AC 2 ARG A 158 ASN A 159 -1 O ARG A 158 N VAL A 132 SITE 1 AC1 11 VAL A 19 TYR A 24 ALA A 40 LYS A 42 SITE 2 AC1 11 GLU A 90 TYR A 91 VAL A 92 ASN A 95 SITE 3 AC1 11 GLU A 98 GLU A 139 CYS A 152 SITE 1 AC2 6 PRO A 231 SER A 232 GLN A 298 GLN A 300 SITE 2 AC2 6 HOH A2098 HOH A2149 SITE 1 AC3 3 ALA A 283 ASP A 284 GLN A 290 SITE 1 AC4 4 GLU A 93 SER A 144 HIS A 145 ARG A 301 SITE 1 AC5 5 HIS A 124 HIS A 127 LYS A 128 LYS A 190 SITE 2 AC5 5 HOH A2152 SITE 1 AC6 5 ALA A 78 GLY A 264 ASN A 267 HOH A2041 SITE 2 AC6 5 HOH A2123 CRYST1 51.942 65.507 102.899 90.00 90.00 90.00 P 21 21 21 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 0.019252 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009718 0.00000