HEADER HYDROLASE 15-APR-19 6RFK TITLE CRYSTAL STRUCTURE OF EGRCK-INHIBITED GLA-DOMAINLESS FIXA (K148Q, R150Q TITLE 2 VARIANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COAGULATION FACTOR IX; COMPND 3 CHAIN: E; COMPND 4 SYNONYM: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC; COMPND 5 EC: 3.4.21.22; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: E. COLI EXPRESSION CONSTRUCT REPLACES THE LEU AT THE COMPND 8 BEGINNING OF THE EGF2 DOMAIN WITH MET.; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: COAGULATION FACTOR IX; COMPND 11 CHAIN: S; COMPND 12 SYNONYM: CHRISTMAS FACTOR,PLASMA THROMBOPLASTIN COMPONENT,PTC; COMPND 13 EC: 3.4.21.22; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: MUTATED AT K148 AND R150 TO Q TO PREVENT AUTOLYSIS.; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: GLU-GLY-AR7-0QE; COMPND 18 CHAIN: I; COMPND 19 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: F9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: F9; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.HUNTINGTON,T.J.SENDALL REVDAT 3 24-JAN-24 6RFK 1 REMARK REVDAT 2 31-JUL-19 6RFK 1 REMARK REVDAT 1 12-JUN-19 6RFK 0 JRNL AUTH T.J.SENDALL,J.A.HUNTINGTON JRNL TITL NMR RESONANCE ASSIGNMENTS OF APO AND EGRCK-INHIBITED FACTOR JRNL TITL 2 IXA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 58601 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) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3114 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4212 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 249 REMARK 3 BIN FREE R VALUE : 0.2880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2264 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 80 REMARK 3 SOLVENT ATOMS : 224 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 0.66000 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): 0.055 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.043 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.013 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2385 ; 0.033 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2204 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3211 ; 2.656 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5056 ; 2.462 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 6.393 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 104 ;32.826 ;24.615 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 359 ;11.522 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;16.625 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2676 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 0.014 ; 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): 1173 ; 5.937 ; 3.028 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1172 ; 5.851 ; 3.029 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1462 ; 6.721 ; 4.529 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1463 ; 6.722 ; 4.530 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1212 ; 8.639 ; 3.644 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1212 ; 8.637 ; 3.644 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1750 ; 9.419 ; 5.227 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2661 ; 8.650 ;38.213 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2616 ; 8.664 ;37.695 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4589 ; 7.282 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 143 ;33.283 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4618 ;20.348 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6RFK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-APR-19. REMARK 100 THE DEPOSITION ID IS D_1200010811. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R CDTE 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61775 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 70.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 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 : 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: 5JB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE PH 8.5, 24% PEG REMARK 280 3350, 0.275M NA MALONATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 45.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.08000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.08000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.08000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.08000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.08000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.08000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.08000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.08000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.87500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 45.75000 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, S, I 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE GLU-GLY-ARG-CHLOROMETHYL KETONE IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: GLU-GLY-ARG-CHLOROMETHYL KETONE REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 MET E 84 CG SD CE REMARK 470 ASP E 85 CG OD1 OD2 REMARK 470 LYS E 91 CE NZ REMARK 470 ARG E 94 CD NE CZ NH1 NH2 REMARK 470 LYS E 100 CD CE NZ REMARK 470 SER E 102 OG REMARK 470 ASP E 104 CG OD1 OD2 REMARK 470 ASN E 105 CG OD1 ND2 REMARK 470 LYS E 106 CG CD CE NZ REMARK 470 GLU E 113 CG CD OE1 OE2 REMARK 470 GLU E 119 CG CD OE1 OE2 REMARK 470 THR E 140 OG1 CG2 REMARK 470 SER E 141 OG REMARK 470 LYS E 142 CG CD CE NZ REMARK 470 LEU E 143 CG CD1 CD2 REMARK 470 THR E 144 OG1 CG2 REMARK 470 ARG E 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS S 23 CE NZ REMARK 470 LYS S 37 CG CD CE NZ REMARK 470 THR S 60A OG1 CG2 REMARK 470 LYS S 82 CD CE NZ REMARK 470 LYS S 98 CD CE NZ REMARK 470 GLN S 150 CG CD OE1 NE2 REMARK 470 LYS S 243 CD CE NZ REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 MET E 84 REMARK 475 ALA E 103 REMARK 475 ASP E 104 REMARK 475 ASN E 105 REMARK 475 THR E 140 REMARK 475 SER E 141 REMARK 475 LYS E 142 REMARK 475 LEU E 143 REMARK 475 THR E 144 REMARK 475 ARG E 145 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP E 85 N CA CB REMARK 480 SER E 102 CA C O CB REMARK 480 LYS E 106 N REMARK 480 GLN E 139 C O REMARK 480 THR S 245 CA C O CB OG1 CG2 OXT 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 S 437 O HOH S 557 1.98 REMARK 500 O1 GOL S 311 O HOH S 401 2.08 REMARK 500 OE2 GLU S 127 O2 GOL S 302 2.14 REMARK 500 OE1 GLU S 217 O3 GOL S 306 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS E 106 N LYS E 106 CA 0.127 REMARK 500 GLU E 125 CG GLU E 125 CD 0.094 REMARK 500 ARG E 134 CZ ARG E 134 NH2 0.090 REMARK 500 CYS S 42 CB CYS S 42 SG 0.115 REMARK 500 SER S 45 CA SER S 45 CB 0.095 REMARK 500 GLU S 60 C GLU S 60 O 0.207 REMARK 500 GLU S 75 CG GLU S 75 CD -0.118 REMARK 500 TYR S 137 CZ TYR S 137 OH -0.128 REMARK 500 ARG S 159 CZ ARG S 159 NH2 0.099 REMARK 500 ARG S 165 CD ARG S 165 NE -0.173 REMARK 500 ARG S 165 CZ ARG S 165 NH2 0.291 REMARK 500 GLU S 186 CD GLU S 186 OE1 0.081 REMARK 500 GLU S 202 CG GLU S 202 CD 0.120 REMARK 500 GLU S 202 CD GLU S 202 OE1 0.123 REMARK 500 GLU S 217 CD GLU S 217 OE1 0.073 REMARK 500 GLU S 240 CD GLU S 240 OE1 0.131 REMARK 500 GLU S 240 CD GLU S 240 OE2 0.080 REMARK 500 GLY I 2 C AR7 I 3 N 0.152 REMARK 500 REMARK 500 REMARK: NULL 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 ASP E 85 CA - C - O ANGL. DEV. = -18.9 DEGREES REMARK 500 ASP E 85 CA - C - N ANGL. DEV. = 20.1 DEGREES REMARK 500 ARG E 134 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 GLY S 35 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ASP S 39 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 CYS S 42 CA - CB - SG ANGL. DEV. = -12.8 DEGREES REMARK 500 GLU S 60 O - C - N ANGL. DEV. = 11.2 DEGREES REMARK 500 GLU S 75 OE1 - CD - OE2 ANGL. DEV. = 10.2 DEGREES REMARK 500 GLU S 77 OE1 - CD - OE2 ANGL. DEV. = -12.2 DEGREES REMARK 500 ARG S 87 NE - CZ - NH2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP S 109 OD1 - CG - OD2 ANGL. DEV. = -11.7 DEGREES REMARK 500 ASP S 109 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 TYR S 137 CZ - CE2 - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG S 159 NE - CZ - NH1 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG S 159 NE - CZ - NH2 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG S 165 CG - CD - NE ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG S 165 NE - CZ - NH1 ANGL. DEV. = -15.3 DEGREES REMARK 500 ARG S 165 NE - CZ - NH2 ANGL. DEV. = 9.8 DEGREES REMARK 500 TYR S 228 CG - CD2 - CE2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG S 233 NE - CZ - NH1 ANGL. DEV. = -3.7 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 GLN E 97 -84.05 -110.40 REMARK 500 GLU S 60 137.31 177.20 REMARK 500 HIS S 71 -62.67 -134.61 REMARK 500 ASN S 115 -164.67 -164.41 REMARK 500 SER S 214 -64.18 -125.51 REMARK 500 GLU S 219 -154.66 56.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY S 35 -13.05 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 CA S 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU S 70 OE1 REMARK 620 2 ASN S 72 O 85.0 REMARK 620 3 GLU S 75 O 160.5 87.1 REMARK 620 4 GLU S 77 OE1 81.0 88.3 116.6 REMARK 620 5 GLU S 77 OE2 129.1 84.0 67.5 49.2 REMARK 620 6 GLU S 80 OE2 99.2 174.6 89.9 89.1 90.7 REMARK 620 7 GOL S 308 O1 80.4 97.1 82.8 160.2 150.3 87.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue B3P E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA S 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL S 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues AR7 I 3 and 0QE I 4 DBREF 6RFK E 84 145 UNP P00740 FA9_HUMAN 130 191 DBREF 6RFK S 16 245 UNP P00740 FA9_HUMAN 227 461 DBREF 6RFK I 1 4 PDB 6RFK 6RFK 1 4 SEQADV 6RFK MET E 84 UNP P00740 LEU 130 CONFLICT SEQADV 6RFK GLN S 148 UNP P00740 LYS 362 ENGINEERED MUTATION SEQADV 6RFK GLN S 150 UNP P00740 ARG 364 ENGINEERED MUTATION SEQRES 1 E 62 MET ASP VAL THR CYS ASN ILE LYS ASN GLY ARG CYS GLU SEQRES 2 E 62 GLN PHE CYS LYS ASN SER ALA ASP ASN LYS VAL VAL CYS SEQRES 3 E 62 SER CYS THR GLU GLY TYR ARG LEU ALA GLU ASN GLN LYS SEQRES 4 E 62 SER CYS GLU PRO ALA VAL PRO PHE PRO CYS GLY ARG VAL SEQRES 5 E 62 SER VAL SER GLN THR SER LYS LEU THR ARG SEQRES 1 S 235 VAL VAL GLY GLY GLU ASP ALA LYS PRO GLY GLN PHE PRO SEQRES 2 S 235 TRP GLN VAL VAL LEU ASN GLY LYS VAL ASP ALA PHE CYS SEQRES 3 S 235 GLY GLY SER ILE VAL ASN GLU LYS TRP ILE VAL THR ALA SEQRES 4 S 235 ALA HIS CYS VAL GLU THR GLY VAL LYS ILE THR VAL VAL SEQRES 5 S 235 ALA GLY GLU HIS ASN ILE GLU GLU THR GLU HIS THR GLU SEQRES 6 S 235 GLN LYS ARG ASN VAL ILE ARG ILE ILE PRO HIS HIS ASN SEQRES 7 S 235 TYR ASN ALA ALA ILE ASN LYS TYR ASN HIS ASP ILE ALA SEQRES 8 S 235 LEU LEU GLU LEU ASP GLU PRO LEU VAL LEU ASN SER TYR SEQRES 9 S 235 VAL THR PRO ILE CYS ILE ALA ASP LYS GLU TYR THR ASN SEQRES 10 S 235 ILE PHE LEU LYS PHE GLY SER GLY TYR VAL SER GLY TRP SEQRES 11 S 235 GLY ARG VAL PHE HIS GLN GLY GLN SER ALA LEU VAL LEU SEQRES 12 S 235 GLN TYR LEU ARG VAL PRO LEU VAL ASP ARG ALA THR CYS SEQRES 13 S 235 LEU ARG SER THR LYS PHE THR ILE TYR ASN ASN MET PHE SEQRES 14 S 235 CYS ALA GLY PHE HIS GLU GLY GLY ARG ASP SER CYS GLN SEQRES 15 S 235 GLY ASP SER GLY GLY PRO HIS VAL THR GLU VAL GLU GLY SEQRES 16 S 235 THR SER PHE LEU THR GLY ILE ILE SER TRP GLY GLU GLU SEQRES 17 S 235 CYS ALA MET LYS GLY LYS TYR GLY ILE TYR THR LYS VAL SEQRES 18 S 235 SER ARG TYR VAL ASN TRP ILE LYS GLU LYS THR LYS LEU SEQRES 19 S 235 THR SEQRES 1 I 4 GLU GLY AR7 0QE HET AR7 I 3 11 HET 0QE I 4 1 HET B3P E 201 19 HET CA S 301 1 HET GOL S 302 6 HET GOL S 303 6 HET GOL S 304 6 HET GOL S 305 6 HET GOL S 306 6 HET GOL S 307 6 HET GOL S 308 6 HET GOL S 309 6 HET GOL S 310 6 HET GOL S 311 6 HETNAM AR7 AMINO{[(4S)-4-AMINO-5,5- HETNAM 2 AR7 DIHYDROXYPENTYL]AMINO}METHANIMINIUM HETNAM 0QE CHLOROMETHANE HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)- HETNAM 2 B3P PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETSYN 0QE CHLORO METHYL GROUP HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 AR7 C6 H17 N4 O2 1+ FORMUL 3 0QE C H3 CL FORMUL 4 B3P C11 H26 N2 O6 FORMUL 5 CA CA 2+ FORMUL 6 GOL 10(C3 H8 O3) FORMUL 16 HOH *224(H2 O) HELIX 1 AA1 ILE E 90 CYS E 95 5 6 HELIX 2 AA2 ALA S 55 VAL S 59 5 5 HELIX 3 AA3 ASP S 125 PHE S 133 1 11 HELIX 4 AA4 ASP S 164 SER S 171 1 8 HELIX 5 AA5 TYR S 234 LYS S 243 1 10 SHEET 1 AA1 2 PHE E 98 SER E 102 0 SHEET 2 AA1 2 LYS E 106 SER E 110 -1 O LYS E 106 N SER E 102 SHEET 1 AA2 2 TYR E 115 LEU E 117 0 SHEET 2 AA2 2 CYS E 124 PRO E 126 -1 O GLU E 125 N ARG E 116 SHEET 1 AA3 8 GLU S 20 ASP S 21 0 SHEET 2 AA3 8 GLN S 156 VAL S 163 -1 O TYR S 157 N GLU S 20 SHEET 3 AA3 8 MET S 180 ALA S 183 -1 O CYS S 182 N VAL S 163 SHEET 4 AA3 8 GLY S 226 LYS S 230 -1 O TYR S 228 N PHE S 181 SHEET 5 AA3 8 THR S 206 GLY S 216 -1 N TRP S 215 O ILE S 227 SHEET 6 AA3 8 PRO S 198 VAL S 203 -1 N VAL S 203 O THR S 206 SHEET 7 AA3 8 SER S 135 GLY S 140 -1 N TYR S 137 O VAL S 200 SHEET 8 AA3 8 GLN S 156 VAL S 163 -1 O VAL S 160 N GLY S 136 SHEET 1 AA4 7 GLN S 30 ASN S 34 0 SHEET 2 AA4 7 CYS S 42 ASN S 48 -1 O GLY S 44 N VAL S 31 SHEET 3 AA4 7 TRP S 51 THR S 54 -1 O TRP S 51 N VAL S 47 SHEET 4 AA4 7 ALA S 104 LEU S 108 -1 O ALA S 104 N THR S 54 SHEET 5 AA4 7 GLN S 81 PRO S 90 -1 N ILE S 89 O LEU S 105 SHEET 6 AA4 7 THR S 65 ALA S 68 -1 N VAL S 66 O ARG S 83 SHEET 7 AA4 7 GLN S 30 ASN S 34 -1 N ASN S 34 O THR S 65 SSBOND 1 CYS E 88 CYS E 99 1555 1555 2.12 SSBOND 2 CYS E 95 CYS E 109 1555 1555 2.06 SSBOND 3 CYS E 111 CYS E 124 1555 1555 2.37 SSBOND 4 CYS E 132 CYS S 122 1555 1555 2.12 SSBOND 5 CYS S 42 CYS S 58 1555 1555 2.18 SSBOND 6 CYS S 168 CYS S 182 1555 1555 2.13 SSBOND 7 CYS S 191 CYS S 220 1555 1555 2.26 LINK NE2 HIS S 57 C1 0QE I 4 1555 1555 1.49 LINK OG SER S 195 C AR7 I 3 1555 1555 1.41 LINK C GLY I 2 N AR7 I 3 1555 1555 1.49 LINK C AR7 I 3 C1 0QE I 4 1555 1555 1.56 LINK OE1 GLU S 70 CA CA S 301 1555 1555 2.32 LINK O ASN S 72 CA CA S 301 1555 1555 2.26 LINK O GLU S 75 CA CA S 301 1555 1555 2.24 LINK OE1 GLU S 77 CA CA S 301 1555 1555 2.34 LINK OE2 GLU S 77 CA CA S 301 1555 1555 2.60 LINK OE2 GLU S 80 CA CA S 301 1555 1555 2.31 LINK CA CA S 301 O1 GOL S 308 1555 1555 2.35 SITE 1 AC1 15 ASN E 92 ARG E 94 CYS E 95 GLU E 96 SITE 2 AC1 15 LYS E 122 SER E 123 HOH E 301 HOH E 308 SITE 3 AC1 15 HOH E 309 HOH E 310 GLU S 204 GOL S 303 SITE 4 AC1 15 HOH S 402 HOH S 497 HOH S 591 SITE 1 AC2 6 GLU S 70 ASN S 72 GLU S 75 GLU S 77 SITE 2 AC2 6 GLU S 80 GOL S 308 SITE 1 AC3 7 CYS E 88 CYS E 99 GLU S 127 TYR S 128 SITE 2 AC3 7 ILE S 129B ARG S 170 HOH S 467 SITE 1 AC4 8 B3P E 201 HIS S 185 GLU S 202 VAL S 203 SITE 2 AC4 8 GLU S 204 HOH S 402 HOH S 483 HOH S 486 SITE 1 AC5 7 GLY S 35 LYS S 37 VAL S 38 PHE S 41 SITE 2 AC5 7 CYS S 58 VAL S 62 LYS S 63 SITE 1 AC6 7 ASN S 97 TYR S 99 PHE S 174 THR S 175 SITE 2 AC6 7 TYR S 177 TRP S 215 HOH S 507 SITE 1 AC7 6 SER S 171 THR S 172 GLY S 216 GLU S 217 SITE 2 AC7 6 LYS S 224 TYR S 225 SITE 1 AC8 3 ASP S 21 LEU S 153 VAL S 154 SITE 1 AC9 7 GLU S 70 ASN S 72 ILE S 73 GLU S 75 SITE 2 AC9 7 GLU S 80 CA S 301 HOH S 489 SITE 1 AD1 5 HIS S 91 ASN S 93 HIS S 101 ARG S 233 SITE 2 AD1 5 HOH S 510 SITE 1 AD2 9 LYS S 126 ASN S 129A LYS S 230 SER S 232 SITE 2 AD2 9 ARG S 233 HOH S 405 HOH S 407 HOH S 546 SITE 3 AD2 9 HOH S 549 SITE 1 AD3 4 LYS S 132 LEU S 162 ASP S 164 HOH S 401 SITE 1 AD4 18 GLU I 1 GLY I 2 HOH I 102 HIS S 57 SITE 2 AD4 18 ASP S 189 SER S 190 CYS S 191 GLN S 192 SITE 3 AD4 18 GLY S 193 SER S 195 SER S 214 TRP S 215 SITE 4 AD4 18 GLY S 216 GLU S 219 CYS S 220 GLY S 226 SITE 5 AD4 18 HOH S 442 HOH S 499 CRYST1 100.160 100.160 91.500 90.00 90.00 90.00 P 43 21 2 8 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 0.009984 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010929 0.00000