HEADER VIRAL PROTEIN 27-SEP-17 5YHA TITLE CRYSTAL STRUCTURE OF PD(ALLYL)/WILD TYPE POLYHEDRA COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYHEDRIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: C-POLYHEDRIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI CYTOPLASMIC POLYHEDROSIS VIRUS; SOURCE 3 ORGANISM_COMMON: BMCPV; SOURCE 4 ORGANISM_TAXID: 110829; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS IN VIVO PROTEIN CRYSTAL, POLYHEDRA, VIRAL PROTEIN, METAL COMPLEXES EXPDTA X-RAY DIFFRACTION AUTHOR S.ABE,K.ATSUMI,K.YAMASHITA,K.HIRATA,H.MORI,T.UENO REVDAT 4 09-OCT-24 5YHA 1 REMARK REVDAT 3 22-NOV-23 5YHA 1 LINK REVDAT 2 14-FEB-18 5YHA 1 JRNL REVDAT 1 29-NOV-17 5YHA 0 JRNL AUTH S.ABE,K.ATSUMI,K.YAMASHITA,K.HIRATA,H.MORI,T.UENO JRNL TITL STRUCTURE OF IN CELL PROTEIN CRYSTALS CONTAINING JRNL TITL 2 ORGANOMETALLIC COMPLEXES. JRNL REF PHYS CHEM CHEM PHYS V. 20 2986 2018 JRNL REFN ESSN 1463-9084 JRNL PMID 29138769 JRNL DOI 10.1039/C7CP06651A REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22665 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2494 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) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1655 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 182 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2009 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.096 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.099 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.153 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2085 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1877 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2832 ; 1.915 ; 1.933 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4303 ; 1.293 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 6.272 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;38.772 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 326 ;13.139 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.073 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 287 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2437 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 543 ; 0.002 ; 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): 991 ; 1.081 ; 1.030 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 990 ; 1.066 ; 1.029 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1237 ; 1.624 ; 1.540 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1238 ; 1.625 ; 1.541 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1093 ; 2.228 ; 1.356 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1093 ; 2.223 ; 1.356 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1574 ; 3.405 ; 1.892 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2463 ; 4.642 ; 9.265 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2464 ; 4.641 ; 9.271 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 : 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: NULL REMARK 4 REMARK 4 5YHA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005262. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-16 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 46.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 46.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 2OH6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: IN VIVO CRYSTALLIZATION, IN CELL, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 15555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 16555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z+1/2,-X+1/2,-Y+1/2 REMARK 290 19555 -Z+1/2,-X+1/2,Y+1/2 REMARK 290 20555 -Z+1/2,X+1/2,-Y+1/2 REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z+1/2,-X+1/2 REMARK 290 23555 Y+1/2,-Z+1/2,-X+1/2 REMARK 290 24555 -Y+1/2,-Z+1/2,X+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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 51.59500 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 51.59500 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 51.59500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 51.59500 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 51.59500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 51.59500 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: 11560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT3 3 1.000000 0.000000 0.000000 0.00000 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 GLU A 171 CD GLU A 171 OE2 -0.123 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 TYR A 57 -54.47 72.40 REMARK 500 SER A 131 34.88 77.47 REMARK 500 GLU A 135 -55.56 76.90 REMARK 500 ASN A 185 85.60 -154.79 REMARK 500 TYR A 224 -58.46 -130.27 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 PD A 306 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 66 NZ REMARK 620 2 CYS A 211 SG 41.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PD A 305 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 76 ND1 REMARK 620 2 HIS A 76 ND1 0.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PD A 308 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 204 SG REMARK 620 2 HOH A 509 O 92.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PLL A 302 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 211 SG REMARK 620 2 PLL A 302 C19 105.5 REMARK 620 3 PLL A 302 C20 170.9 79.7 REMARK 620 4 PLL A 302 C21 142.9 45.3 45.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PLL A 303 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 211 SG REMARK 620 2 PLL A 303 C19 159.0 REMARK 620 3 PLL A 303 C20 99.8 80.0 REMARK 620 4 PLL A 303 C21 120.2 46.0 45.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 PLL A 304 PD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 238 NE2 REMARK 620 2 PLL A 304 C19 158.2 REMARK 620 3 PLL A 304 C20 116.6 81.3 REMARK 620 4 PLL A 304 C21 139.2 45.3 46.3 REMARK 620 5 HOH A 411 O 66.2 130.6 86.6 131.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PD A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310 DBREF 5YHA A 2 248 UNP P11041 PYHD_CPVBM 2 248 SEQADV 5YHA ACE A 1 UNP P11041 ACETYLATION SEQRES 1 A 248 ACE ALA ASP VAL ALA GLY THR SER ASN ARG ASP PHE ARG SEQRES 2 A 248 GLY ARG GLU GLN ARG LEU PHE ASN SER GLU GLN TYR ASN SEQRES 3 A 248 TYR ASN ASN SER LEU ASN GLY GLU VAL SER VAL TRP VAL SEQRES 4 A 248 TYR ALA TYR TYR SER ASP GLY SER VAL LEU VAL ILE ASN SEQRES 5 A 248 LYS ASN SER GLN TYR LYS VAL GLY ILE SER GLU THR PHE SEQRES 6 A 248 LYS ALA LEU LYS GLU TYR ARG GLU GLY GLN HIS ASN ASP SEQRES 7 A 248 SER TYR ASP GLU TYR GLU VAL ASN GLN SER ILE TYR TYR SEQRES 8 A 248 PRO ASN GLY GLY ASP ALA ARG LYS PHE HIS SER ASN ALA SEQRES 9 A 248 LYS PRO ARG ALA ILE GLN ILE ILE PHE SER PRO SER VAL SEQRES 10 A 248 ASN VAL ARG THR ILE LYS MET ALA LYS GLY ASN ALA VAL SEQRES 11 A 248 SER VAL PRO ASP GLU TYR LEU GLN ARG SER HIS PRO TRP SEQRES 12 A 248 GLU ALA THR GLY ILE LYS TYR ARG LYS ILE LYS ARG ASP SEQRES 13 A 248 GLY GLU ILE VAL GLY TYR SER HIS TYR PHE GLU LEU PRO SEQRES 14 A 248 HIS GLU TYR ASN SER ILE SER LEU ALA VAL SER GLY VAL SEQRES 15 A 248 HIS LYS ASN PRO SER SER TYR ASN VAL GLY SER ALA HIS SEQRES 16 A 248 ASN VAL MET ASP VAL PHE GLN SER CYS ASP LEU ALA LEU SEQRES 17 A 248 ARG PHE CYS ASN ARG TYR TRP ALA GLU LEU GLU LEU VAL SEQRES 18 A 248 ASN HIS TYR ILE SER PRO ASN ALA TYR PRO TYR LEU ASP SEQRES 19 A 248 ILE ASN ASN HIS SER TYR GLY VAL ALA LEU SER ASN ARG SEQRES 20 A 248 GLN HET ACE A 1 3 HET CL A 301 1 HET PLL A 302 4 HET PLL A 303 4 HET PLL A 304 4 HET PD A 305 1 HET PD A 306 1 HET PD A 307 1 HET PD A 308 1 HET PD A 309 1 HET EDO A 310 4 HETNAM ACE ACETYL GROUP HETNAM CL CHLORIDE ION HETNAM PLL PALLADIUM(II) ALLYL COMPLEX HETNAM PD PALLADIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 ACE C2 H4 O FORMUL 2 CL CL 1- FORMUL 3 PLL 3(C3 H5 PD) FORMUL 6 PD 5(PD 2+) FORMUL 11 EDO C2 H6 O2 FORMUL 12 HOH *111(H2 O) HELIX 1 AA1 ASP A 11 SER A 30 1 20 HELIX 2 AA2 THR A 64 LYS A 69 1 6 HELIX 3 AA3 ASP A 78 TYR A 91 1 14 HELIX 4 AA4 ASN A 118 ILE A 122 5 5 HELIX 5 AA5 TYR A 136 SER A 140 5 5 HELIX 6 AA6 THR A 146 TYR A 150 5 5 HELIX 7 AA7 ASN A 196 ALA A 207 1 12 HELIX 8 AA8 ALA A 216 TYR A 224 1 9 SHEET 1 AA1 6 ARG A 151 ARG A 155 0 SHEET 2 AA1 6 GLU A 158 GLU A 167 -1 O VAL A 160 N ILE A 153 SHEET 3 AA1 6 ALA A 108 PHE A 113 -1 N ILE A 111 O HIS A 164 SHEET 4 AA1 6 GLU A 34 TYR A 42 -1 N TYR A 40 O GLN A 110 SHEET 5 AA1 6 VAL A 48 GLN A 56 -1 O ILE A 51 N VAL A 39 SHEET 6 AA1 6 LEU A 208 TYR A 214 -1 O TYR A 214 N VAL A 48 SHEET 1 AA2 3 LYS A 58 GLU A 63 0 SHEET 2 AA2 3 SER A 176 VAL A 182 -1 O LEU A 177 N GLU A 63 SHEET 3 AA2 3 LYS A 123 GLY A 127 -1 N ALA A 125 O ALA A 178 SHEET 1 AA3 2 TYR A 232 LEU A 233 0 SHEET 2 AA3 2 SER A 239 TYR A 240 -1 O TYR A 240 N TYR A 232 LINK C ACE A 1 N ALA A 2 1555 1555 1.33 LINK NZ LYS A 66 PD PD A 306 1555 5555 2.80 LINK ND1 HIS A 76 PD PD A 305 1555 1555 2.48 LINK ND1 HIS A 76 PD PD A 305 1555 2665 2.12 LINK NE2 HIS A 170 PD PD A 307 1555 1555 2.31 LINK SG CYS A 204 PD PD A 308 1555 1555 2.49 LINK SG CYS A 211 PD PLL A 302 1555 1555 2.19 LINK SG CYS A 211 PD PLL A 303 1555 1555 2.43 LINK SG CYS A 211 PD PD A 306 1555 1555 2.25 LINK NE2 HIS A 238 PD PLL A 304 1555 1555 2.53 LINK ND1 HIS A 238 PD PD A 309 1555 1555 2.73 LINK PD PLL A 304 O HOH A 411 1555 1555 2.24 LINK PD PD A 308 O HOH A 509 1555 1555 2.42 SITE 1 AC1 2 ALA A 2 LEU A 31 SITE 1 AC2 3 ARG A 209 CYS A 211 PLL A 303 SITE 1 AC3 4 GLU A 63 CYS A 211 PLL A 302 PD A 306 SITE 1 AC4 7 HIS A 141 TRP A 143 GLU A 144 ARG A 155 SITE 2 AC4 7 HIS A 238 SER A 239 HOH A 411 SITE 1 AC5 1 HIS A 76 SITE 1 AC6 3 LYS A 66 CYS A 211 PLL A 303 SITE 1 AC7 1 HIS A 170 SITE 1 AC8 3 LYS A 58 CYS A 204 HOH A 509 SITE 1 AC9 1 HIS A 238 SITE 1 AD1 6 ASP A 3 GLY A 46 PHE A 100 ALA A 216 SITE 2 AD1 6 GLU A 217 HOH A 421 CRYST1 103.190 103.190 103.190 90.00 90.00 90.00 I 2 3 24 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 0.009691 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009691 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009691 0.00000 HETATM 1 C ACE A 1 68.224 -10.936 9.371 1.00 22.54 C HETATM 2 O ACE A 1 67.686 -11.167 8.316 1.00 24.54 O HETATM 3 CH3 ACE A 1 69.244 -11.886 9.929 1.00 26.02 C