HEADER TRANSFERASE 16-JAN-08 3BYV TITLE CRYSTAL STRUCTURE OF TOXOPLASMA GONDII SPECIFIC RHOPTRY ANTIGEN KINASE TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHOPTRY KINASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 210-568; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII; SOURCE 3 ORGANISM_TAXID: 5811; SOURCE 4 GENE: 33.M00005; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOXOPLASMA, 33.M00005, RHOPTRY, MALARIA, KINASE, TRANSFERASE, KEYWDS 2 STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR A.K.WERNIMONT,V.V.LUNIN,C.YANG,J.LEW,I.KOZIERADZKI,Y.H.LIN,X.SUN, AUTHOR 2 C.KHUU,Y.ZHAO,M.SCHAPIRA,C.H.ARROWSMITH,A.M.EDWARDS,J.WEIGELT, AUTHOR 3 A.BOCHKAREV,R.HUI,D.SIBLEY,W.QIU,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 4 (SGC) REVDAT 4 30-OCT-24 3BYV 1 REMARK SEQADV LINK REVDAT 3 01-SEP-09 3BYV 1 JRNL REVDAT 2 24-FEB-09 3BYV 1 VERSN REVDAT 1 29-JAN-08 3BYV 0 JRNL AUTH W.QIU,A.WERNIMONT,K.TANG,S.TAYLOR,V.LUNIN,M.SCHAPIRA, JRNL AUTH 2 S.FENTRESS,R.HUI,L.D.SIBLEY JRNL TITL NOVEL STRUCTURAL AND REGULATORY FEATURES OF RHOPTRY JRNL TITL 2 SECRETORY KINASES IN TOXOPLASMA GONDII. JRNL REF EMBO J. V. 28 969 2009 JRNL REFN ISSN 0261-4189 JRNL PMID 19197235 JRNL DOI 10.1038/EMBOJ.2009.24 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31731 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1692 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2313 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.02000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.484 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2932 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3979 ; 2.367 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 354 ; 8.639 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;33.950 ;22.446 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 502 ;17.357 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.926 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 441 ; 0.189 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2216 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1404 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1954 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 164 ; 0.205 ; 0.200 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): 57 ; 0.265 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.372 ; 0.200 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): 1815 ; 1.495 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2835 ; 2.056 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1297 ; 3.289 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1137 ; 4.750 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3BYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000046128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-07; 17-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : CHESS; ROTATING ANODE REMARK 200 BEAMLINE : A1; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; RIGAKU FR-E+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978; 2.29 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; RIGAKU RAXIS REMARK 200 IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33484 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.48600 REMARK 200 R SYM FOR SHELL (I) : 0.42700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.210 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M MGNO3, 0.1 M TRIS REMARK 280 -HCL PH 8.5, 1 MM MGCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K. 24% PEG 3350, 0.2 M MGNO3, 0.1 M TRIS-HCL PH REMARK 280 8.5, 1 MM MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 29.53600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.70900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.91050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.70900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.53600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.91050 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 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 MET A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 HIS A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 SER A 199 REMARK 465 SER A 200 REMARK 465 GLY A 201 REMARK 465 ARG A 202 REMARK 465 GLU A 203 REMARK 465 ASN A 204 REMARK 465 LEU A 205 REMARK 465 TYR A 206 REMARK 465 PHE A 207 REMARK 465 TYR A 233 REMARK 465 THR A 249 REMARK 465 GLN A 286 REMARK 465 ARG A 302 REMARK 465 ARG A 355 REMARK 465 LEU A 356 REMARK 465 ASP A 357 REMARK 465 GLU A 358 REMARK 465 ARG A 359 REMARK 465 ASP A 360 REMARK 465 THR A 505 REMARK 465 LYS A 506 REMARK 465 ASP A 507 REMARK 465 ALA A 508 REMARK 465 ALA A 509 REMARK 465 LEU A 510 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 SER A 231 OG REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 319 NE CZ NH1 NH2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 GLU A 514 CD OE1 OE2 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 815 O HOH A 842 1.57 REMARK 500 NH2 ARG A 558 O HOH A 810 2.08 REMARK 500 O HOH A 761 O HOH A 781 2.09 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 O HOH A 740 O HOH A 855 4455 1.99 REMARK 500 O HOH A 819 O HOH A 855 4455 2.19 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 TYR A 280 CD1 TYR A 280 CE1 0.096 REMARK 500 VAL A 354 C VAL A 354 O 0.193 REMARK 500 SER A 412 CB SER A 412 OG -0.090 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 A 212 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 GLY A 260 N - CA - C ANGL. DEV. = -25.9 DEGREES REMARK 500 LEU A 281 CA - CB - CG ANGL. DEV. = 16.4 DEGREES REMARK 500 ASP A 345 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 345 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 476 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 477 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG A 477 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 LEU A 480 CB - CG - CD2 ANGL. DEV. = -10.5 DEGREES REMARK 500 ASP A 486 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU A 502 CB - CG - CD2 ANGL. DEV. = 10.9 DEGREES REMARK 500 LYS A 539 CD - CE - NZ ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 558 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ASN A 226 59.61 -98.29 REMARK 500 LEU A 246 -76.33 -124.82 REMARK 500 ASP A 276 130.37 -38.86 REMARK 500 PRO A 277 37.47 -97.63 REMARK 500 THR A 421 -11.69 81.95 REMARK 500 TYR A 422 59.43 -150.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 259 GLY A 260 101.30 REMARK 500 PHE A 292 GLU A 293 149.93 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 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 442 OE2 REMARK 620 2 HOH A 745 O 94.5 REMARK 620 3 HOH A 793 O 173.6 87.9 REMARK 620 4 HOH A 802 O 85.8 91.6 88.3 REMARK 620 5 HOH A 803 O 87.5 176.5 90.4 91.4 REMARK 620 6 HOH A 859 O 95.3 88.1 90.6 178.9 88.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 604 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT REMARK 999 THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) REMARK 999 AT THE TIME OF DEPOSITION. DBREF 3BYV A 192 568 PDB 3BYV 3BYV 192 568 SEQADV 3BYV MET A 192 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 193 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 194 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 195 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 196 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 197 PDB 3BYV EXPRESSION TAG SEQADV 3BYV HIS A 198 PDB 3BYV EXPRESSION TAG SEQADV 3BYV SER A 199 PDB 3BYV EXPRESSION TAG SEQADV 3BYV SER A 200 PDB 3BYV EXPRESSION TAG SEQADV 3BYV GLY A 201 PDB 3BYV EXPRESSION TAG SEQADV 3BYV ARG A 202 PDB 3BYV EXPRESSION TAG SEQADV 3BYV GLU A 203 PDB 3BYV EXPRESSION TAG SEQADV 3BYV ASN A 204 PDB 3BYV EXPRESSION TAG SEQADV 3BYV LEU A 205 PDB 3BYV EXPRESSION TAG SEQADV 3BYV TYR A 206 PDB 3BYV EXPRESSION TAG SEQADV 3BYV PHE A 207 PDB 3BYV EXPRESSION TAG SEQADV 3BYV GLN A 208 PDB 3BYV EXPRESSION TAG SEQADV 3BYV GLY A 209 PDB 3BYV EXPRESSION TAG SEQRES 1 A 377 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 377 LEU TYR PHE GLN GLY PRO GLY ASP VAL VAL ILE GLU GLU SEQRES 3 A 377 LEU PHE ASN ARG ILE PRO GLN ALA ASN VAL ARG THR THR SEQRES 4 A 377 SER GLU TYR MET GLN SER ALA ALA ASP SER LEU VAL SER SEQRES 5 A 377 THR SER LEU TRP ASN THR GLY GLN PRO PHE ARG VAL GLU SEQRES 6 A 377 SER GLU LEU GLY GLU ARG PRO ARG THR LEU VAL ARG GLY SEQRES 7 A 377 THR VAL LEU GLY GLN GLU ASP PRO TYR ALA TYR LEU GLU SEQRES 8 A 377 ALA THR ASP GLN GLU THR GLY GLU SER PHE GLU VAL HIS SEQRES 9 A 377 VAL PRO TYR PHE THR GLU ARG PRO PRO SER ASN ALA ILE SEQRES 10 A 377 LYS GLN MET LYS GLU GLU VAL LEU ARG LEU ARG LEU LEU SEQRES 11 A 377 ARG GLY ILE LYS ASN GLN LYS GLN ALA LYS VAL HIS LEU SEQRES 12 A 377 ARG PHE ILE PHE PRO PHE ASP LEU VAL LYS ASP PRO GLN SEQRES 13 A 377 LYS LYS LYS MET ILE ARG VAL ARG LEU ASP GLU ARG ASP SEQRES 14 A 377 MET TRP VAL LEU SER ARG PHE PHE LEU TYR PRO ARG MET SEQRES 15 A 377 GLN SER ASN LEU GLN THR PHE GLY GLU VAL LEU LEU SER SEQRES 16 A 377 HIS SER SER THR HIS LYS SER LEU VAL HIS HIS ALA ARG SEQRES 17 A 377 LEU GLN LEU THR LEU GLN VAL ILE ARG LEU LEU ALA SER SEQRES 18 A 377 LEU HIS HIS TYR GLY LEU VAL HIS THR TYR LEU ARG PRO SEQRES 19 A 377 VAL ASP ILE VAL LEU ASP GLN ARG GLY GLY VAL PHE LEU SEQRES 20 A 377 THR GLY PHE GLU HIS LEU VAL ARG ASP GLY ALA ARG VAL SEQRES 21 A 377 VAL SER SER VAL SER ARG GLY PHE GLU PRO PRO GLU LEU SEQRES 22 A 377 GLU ALA ARG ARG ALA THR ILE SER TYR HIS ARG ASP ARG SEQRES 23 A 377 ARG THR LEU MET THR PHE SER PHE ASP ALA TRP ALA LEU SEQRES 24 A 377 GLY LEU VAL ILE TYR TRP ILE TRP CYS ALA ASP LEU PRO SEQRES 25 A 377 ILE THR LYS ASP ALA ALA LEU GLY GLY SER GLU TRP ILE SEQRES 26 A 377 PHE ARG SER CYS LYS ASN ILE PRO GLN PRO VAL ARG ALA SEQRES 27 A 377 LEU LEU GLU GLY PHE LEU ARG TYR PRO LYS GLU ASP ARG SEQRES 28 A 377 LEU LEU PRO LEU GLN ALA MET GLU THR PRO GLU TYR GLU SEQRES 29 A 377 GLN LEU ARG THR GLU LEU SER ALA ALA LEU PRO LEU TYR HET MG A 601 1 HET EDO A 602 4 HET EDO A 603 4 HET EDO A 604 4 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG MG 2+ FORMUL 3 EDO 3(C2 H6 O2) FORMUL 6 HOH *164(H2 O) HELIX 1 1 GLY A 211 ILE A 222 1 12 HELIX 2 2 PRO A 223 ASN A 226 5 4 HELIX 3 3 MET A 234 LEU A 246 1 13 HELIX 4 4 ASN A 306 ARG A 317 1 12 HELIX 5 5 LEU A 318 LEU A 321 5 4 HELIX 6 6 ASN A 326 ARG A 335 1 10 HELIX 7 7 LEU A 377 HIS A 387 1 11 HELIX 8 8 HIS A 391 TYR A 416 1 26 HELIX 9 9 ARG A 424 VAL A 426 5 3 HELIX 10 10 GLY A 440 LEU A 444 5 5 HELIX 11 11 PRO A 461 ALA A 469 1 9 HELIX 12 12 ILE A 471 ASP A 476 1 6 HELIX 13 13 THR A 482 ALA A 500 1 19 HELIX 14 14 SER A 513 ARG A 518 5 6 HELIX 15 15 PRO A 524 LEU A 535 1 12 HELIX 16 16 PRO A 538 ARG A 542 5 5 HELIX 17 17 LEU A 544 GLU A 550 1 7 HELIX 18 18 THR A 551 LEU A 565 1 15 HELIX 19 19 PRO A 566 TYR A 568 5 3 SHEET 1 A 9 MET A 351 ILE A 352 0 SHEET 2 A 9 TRP A 362 LEU A 364 -1 O VAL A 363 N ILE A 352 SHEET 3 A 9 SER A 291 PHE A 299 -1 N PHE A 299 O TRP A 362 SHEET 4 A 9 ARG A 366 PRO A 371 -1 O PHE A 368 N HIS A 295 SHEET 5 A 9 ASP A 341 LYS A 344 -1 N VAL A 343 O PHE A 367 SHEET 6 A 9 PRO A 252 SER A 257 -1 N GLU A 256 O LYS A 344 SHEET 7 A 9 ARG A 264 GLU A 275 -1 O LEU A 266 N PHE A 253 SHEET 8 A 9 TYR A 278 THR A 284 -1 O GLU A 282 N GLY A 269 SHEET 9 A 9 SER A 291 PHE A 299 -1 O VAL A 294 N LEU A 281 SHEET 1 B 3 SER A 375 ASN A 376 0 SHEET 2 B 3 ILE A 428 LEU A 430 -1 O LEU A 430 N SER A 375 SHEET 3 B 3 VAL A 436 LEU A 438 -1 O PHE A 437 N VAL A 429 SHEET 1 C 2 LEU A 418 VAL A 419 0 SHEET 2 C 2 VAL A 445 ARG A 446 -1 O VAL A 445 N VAL A 419 SHEET 1 D 2 ARG A 450 VAL A 452 0 SHEET 2 D 2 ARG A 478 LEU A 480 -1 O THR A 479 N VAL A 451 SSBOND 1 CYS A 499 CYS A 520 1555 1555 1.96 LINK OE2 GLU A 442 MG MG A 601 1555 1555 1.99 LINK MG MG A 601 O HOH A 745 1555 1555 2.22 LINK MG MG A 601 O HOH A 793 1555 1555 2.31 LINK MG MG A 601 O HOH A 802 1555 1555 2.23 LINK MG MG A 601 O HOH A 803 1555 1555 2.20 LINK MG MG A 601 O HOH A 859 1555 1555 2.16 CISPEP 1 ASP A 276 PRO A 277 0 -0.07 SITE 1 AC1 6 GLU A 442 HOH A 745 HOH A 793 HOH A 802 SITE 2 AC1 6 HOH A 803 HOH A 859 SITE 1 AC2 7 GLU A 293 HIS A 295 TYR A 370 PRO A 371 SITE 2 AC2 7 MET A 373 HOH A 750 HOH A 817 SITE 1 AC3 6 LYS A 328 VAL A 332 SER A 393 HIS A 397 SITE 2 AC3 6 HOH A 743 HOH A 855 SITE 1 AC4 6 TYR A 278 PHE A 299 ALA A 307 GLN A 310 SITE 2 AC4 6 MET A 311 HOH A 834 CRYST1 59.072 69.821 85.418 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 0.016928 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014322 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011707 0.00000