HEADER OXIDOREDUCTASE 28-MAR-03 1UB2 TITLE CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE FROM SYNECHOCOCCUS PCC 7942 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALASE-PEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.6; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS; SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 STRAIN: PCC 7942; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-3A KEYWDS CATALASE-PEROXIDASE, CATALASE, PEROXIDASE, KATG, SYNECHOCOCCUS PCC KEYWDS 2 7942, CYANOBACTERIA, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.WADA,T.TADA REVDAT 5 23-OCT-24 1UB2 1 REMARK REVDAT 4 25-OCT-23 1UB2 1 REMARK LINK REVDAT 3 13-JUL-11 1UB2 1 VERSN REVDAT 2 24-FEB-09 1UB2 1 VERSN REVDAT 1 28-MAR-04 1UB2 0 JRNL AUTH K.WADA,T.TADA JRNL TITL CRYSTAL STRUCTURE OF CATALASE-PEROXIDASE FROM SYNECHOCOCCUS JRNL TITL 2 PCC 7942 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3013434.830 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 46013 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 SET) : 0.199 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4630 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6620 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 720 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5497 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 703 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.88000 REMARK 3 B22 (A**2) : 5.88000 REMARK 3 B33 (A**2) : -11.76000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.27 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.480 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ANISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.470 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.210 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.750 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.590 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 47.50 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : HEC_XPLOR_PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : HEC_XPLOR_TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000005637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46151 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 19.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21400 REMARK 200 R SYM FOR SHELL (I) : 0.21400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1ITK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PH 6.3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 101.33050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 54.60400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 54.60400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.66525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 54.60400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 54.60400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 151.99575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 54.60400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.60400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.66525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 54.60400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.60400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 151.99575 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 101.33050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -202.66100 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 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 GLN A 5 REMARK 465 GLY A 6 REMARK 465 LYS A 7 REMARK 465 CYS A 8 REMARK 465 PRO A 9 REMARK 465 VAL A 10 REMARK 465 MET A 11 REMARK 465 HIS A 12 REMARK 465 GLY A 13 REMARK 465 GLY A 14 REMARK 465 ALA A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 VAL A 18 REMARK 465 ASN A 19 REMARK 465 ILE A 20 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 CYS A 328 N SER A 329 1.52 REMARK 500 O ALA A 326 N VAL A 327 1.67 REMARK 500 O GLY A 308 ND2 ASN A 339 1.83 REMARK 500 O TYR A 324 O CYS A 328 2.02 REMARK 500 O HIS A 624 O THR A 670 2.05 REMARK 500 O ARG A 486 N LEU A 489 2.16 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 ALA A 326 C VAL A 327 N -0.321 REMARK 500 VAL A 327 C CYS A 328 N 0.178 REMARK 500 CYS A 328 C SER A 329 N -0.211 REMARK 500 ASN A 483 C ASN A 483 O 0.146 REMARK 500 ASN A 483 C GLY A 484 N -0.312 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 GLU A 24 N - CA - C ANGL. DEV. = -19.9 DEGREES REMARK 500 PHE A 192 CB - CG - CD2 ANGL. DEV. = 4.3 DEGREES REMARK 500 ASN A 210 N - CA - C ANGL. DEV. = 17.9 DEGREES REMARK 500 TYR A 221 CD1 - CE1 - CZ ANGL. DEV. = 5.8 DEGREES REMARK 500 ALA A 326 CA - C - N ANGL. DEV. = 23.9 DEGREES REMARK 500 ALA A 326 O - C - N ANGL. DEV. = -27.2 DEGREES REMARK 500 VAL A 327 C - N - CA ANGL. DEV. = 51.5 DEGREES REMARK 500 VAL A 327 CG1 - CB - CG2 ANGL. DEV. = -12.5 DEGREES REMARK 500 CYS A 328 CA - C - N ANGL. DEV. = 25.7 DEGREES REMARK 500 CYS A 328 O - C - N ANGL. DEV. = -42.5 DEGREES REMARK 500 SER A 329 C - N - CA ANGL. DEV. = 18.5 DEGREES REMARK 500 VAL A 370 CB - CA - C ANGL. DEV. = -11.9 DEGREES REMARK 500 ASN A 483 CA - C - N ANGL. DEV. = 24.0 DEGREES REMARK 500 ASN A 483 O - C - N ANGL. DEV. = -26.1 DEGREES REMARK 500 GLY A 484 C - N - CA ANGL. DEV. = 46.3 DEGREES REMARK 500 LEU A 587 CA - CB - CG ANGL. DEV. = -16.1 DEGREES REMARK 500 VAL A 626 CB - CA - C ANGL. DEV. = 12.7 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 THR A 22 -8.21 -38.73 REMARK 500 ALA A 23 80.55 -171.13 REMARK 500 ALA A 61 34.37 -70.11 REMARK 500 ASP A 72 70.52 -110.15 REMARK 500 TRP A 77 70.87 -165.08 REMARK 500 THR A 196 72.80 -109.92 REMARK 500 TYR A 221 -64.31 -120.23 REMARK 500 ASN A 270 73.59 -104.35 REMARK 500 THR A 306 -86.09 -125.21 REMARK 500 HIS A 316 77.63 -112.85 REMARK 500 ASP A 321 -165.15 -167.43 REMARK 500 VAL A 327 -25.26 -24.44 REMARK 500 SER A 329 -30.43 -33.90 REMARK 500 ARG A 367 -156.78 -119.11 REMARK 500 PRO A 435 134.33 -39.12 REMARK 500 TYR A 443 4.30 -153.95 REMARK 500 ASP A 444 93.50 64.65 REMARK 500 ILE A 487 -30.25 -39.22 REMARK 500 GLU A 499 75.92 48.92 REMARK 500 ASP A 573 99.54 -161.34 REMARK 500 THR A 577 57.94 33.61 REMARK 500 ASN A 636 30.72 -94.15 REMARK 500 ALA A 652 59.48 -142.11 REMARK 500 SER A 680 -51.52 -123.55 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 ALA A 326 VAL A 327 -81.06 REMARK 500 CYS A 328 SER A 329 -105.82 REMARK 500 ASN A 483 GLY A 484 -104.68 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 ALA A 326 -10.40 REMARK 500 VAL A 327 16.88 REMARK 500 CYS A 328 -35.27 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 HEM A 721 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 262 NE2 REMARK 620 2 HEM A 721 NA 96.9 REMARK 620 3 HEM A 721 NB 84.9 92.1 REMARK 620 4 HEM A 721 NC 87.5 175.5 89.2 REMARK 620 5 HEM A 721 ND 94.1 90.9 177.0 88.0 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 HEM A 721 DBREF 1UB2 A 1 720 UNP Q55110 Q55110_SYNSP 1 720 SEQRES 1 A 720 MET THR ALA THR GLN GLY LYS CYS PRO VAL MET HIS GLY SEQRES 2 A 720 GLY ALA THR THR VAL ASN ILE SER THR ALA GLU TRP TRP SEQRES 3 A 720 PRO LYS ALA LEU ASN LEU ASP ILE LEU SER GLN HIS ASP SEQRES 4 A 720 ARG LYS THR ASN PRO MET GLY PRO ASP PHE ASN TYR GLN SEQRES 5 A 720 GLU GLU VAL GLN LYS LEU ASP ALA ALA LEU LYS GLN ASP SEQRES 6 A 720 LEU GLN ALA LEU MET THR ASP SER GLN ASP TRP TRP PRO SEQRES 7 A 720 ALA ASP TRP GLY HIS TYR GLY GLY LEU MET ILE ARG LEU SEQRES 8 A 720 THR TRP HIS ALA ALA GLY THR TYR ARG ILE ALA ASP GLY SEQRES 9 A 720 ARG GLY GLY ALA GLY THR GLY ASN GLN ARG PHE ALA PRO SEQRES 10 A 720 LEU ASN SER TRP PRO ASP ASN THR ASN LEU ASP LYS ALA SEQRES 11 A 720 ARG ARG LEU LEU TRP PRO ILE LYS GLN LYS TYR GLY ASN SEQRES 12 A 720 LYS LEU SER TRP ALA ASP LEU ILE ALA TYR ALA GLY THR SEQRES 13 A 720 ILE ALA TYR GLU SER MET GLY LEU LYS THR PHE GLY PHE SEQRES 14 A 720 ALA PHE GLY ARG GLU ASP ILE TRP HIS PRO GLU LYS ASP SEQRES 15 A 720 ILE TYR TRP GLY PRO GLU LYS GLU TRP PHE PRO PRO SER SEQRES 16 A 720 THR ASN PRO ASN SER ARG TYR THR GLY ASP ARG GLU LEU SEQRES 17 A 720 GLU ASN PRO LEU ALA ALA VAL THR MET GLY LEU ILE TYR SEQRES 18 A 720 VAL ASN PRO GLU GLY VAL ASP GLY ASN PRO ASP PRO LEU SEQRES 19 A 720 LYS THR ALA HIS ASP VAL ARG VAL THR PHE ALA ARG MET SEQRES 20 A 720 ALA MET ASN ASP GLU GLU THR VAL ALA LEU THR ALA GLY SEQRES 21 A 720 GLY HIS THR VAL GLY LYS CYS HIS GLY ASN GLY ASN ALA SEQRES 22 A 720 ALA LEU LEU GLY PRO GLU PRO GLU GLY ALA ASP VAL GLU SEQRES 23 A 720 ASP GLN GLY LEU GLY TRP ILE ASN LYS THR GLN SER GLY SEQRES 24 A 720 ILE GLY ARG ASN ALA VAL THR SER GLY LEU GLU GLY ALA SEQRES 25 A 720 TRP THR PRO HIS PRO THR GLN TRP ASP ASN GLY TYR PHE SEQRES 26 A 720 ALA VAL CYS SER LEU ASN TYR ASP TRP GLU LEU LYS LYS SEQRES 27 A 720 ASN PRO ALA GLY ALA TRP GLN TRP GLU PRO ILE ASN PRO SEQRES 28 A 720 ARG GLU GLU ASP LEU PRO VAL ASP VAL GLU ASP PRO SER SEQRES 29 A 720 ILE ARG ARG ASN LEU VAL MET THR ASP ALA ASP MET ALA SEQRES 30 A 720 MET LYS MET ASP PRO GLU TYR ARG LYS ILE SER GLU ARG SEQRES 31 A 720 PHE TYR GLN ASP PRO ALA TYR PHE ALA ASP VAL PHE ALA SEQRES 32 A 720 ARG ALA TRP PHE LYS LEU THR HIS ARG ASP MET GLY PRO SEQRES 33 A 720 LYS ALA ARG TYR ILE GLY PRO ASP VAL PRO GLN GLU ASP SEQRES 34 A 720 LEU ILE TRP GLN ASP PRO ILE PRO ALA GLY ASN ARG ASN SEQRES 35 A 720 TYR ASP VAL GLN ALA VAL LYS ASP ARG ILE ALA ALA SER SEQRES 36 A 720 GLY LEU SER ILE SER GLU LEU VAL SER THR ALA TRP ASP SEQRES 37 A 720 SER ALA ARG THR TYR ARG ASN SER ASP LYS ARG GLY GLY SEQRES 38 A 720 ALA ASN GLY ALA ARG ILE ARG LEU ALA PRO GLN LYS ASP SEQRES 39 A 720 TRP GLU GLY ASN GLU PRO ASP ARG LEU PRO LYS VAL LEU SEQRES 40 A 720 ALA VAL LEU GLU GLY ILE SER ALA ALA THR GLY ALA THR SEQRES 41 A 720 VAL ALA ASP VAL ILE VAL LEU ALA GLY ASN VAL GLY VAL SEQRES 42 A 720 GLU GLN LYS ALA ARG ALA ALA GLY VAL GLU ILE VAL LEU SEQRES 43 A 720 PRO PHE ALA PRO GLY ARG GLY ASP ALA THR ALA GLU GLN SEQRES 44 A 720 THR ASP THR GLU SER PHE ALA VAL LEU GLU PRO ILE HIS SEQRES 45 A 720 ASP ALA ILE ALA THR GLY SER SER ARG THR MET ARG GLN SEQRES 46 A 720 ARG LEU LYS ASN CYS CYS LEU ILE ALA THR GLN LEU LEU SEQRES 47 A 720 GLY LEU THR ALA PRO GLU MET THR VAL LEU ILE GLY GLY SEQRES 48 A 720 LEU ARG VAL LEU GLY THR ASN HIS GLY GLY THR LYS HIS SEQRES 49 A 720 VAL VAL PHE THR ASP ARG GLU GLY VAL LEU THR ASN ASP SEQRES 50 A 720 PHE PHE VAL ASN LEU THR ASP MET ASN TYR LEU TRP LYS SEQRES 51 A 720 PRO ALA GLY LYS ASN LEU TYR GLU ILE CYS ASP ARG LYS SEQRES 52 A 720 THR ASN GLN VAL LYS TRP THR ALA THR ARG VAL ASP LEU SEQRES 53 A 720 VAL PHE GLY SER ASN SER ILE LEU ARG ALA TYR SER GLU SEQRES 54 A 720 LEU TYR ALA GLN ASP ASP ASN LYS GLU LYS PHE VAL ARG SEQRES 55 A 720 ASP PHE VAL ALA ALA TRP THR LYS VAL MET ASN ALA ASP SEQRES 56 A 720 ARG PHE ASP LEU ASP HET HEM A 721 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *703(H2 O) HELIX 1 1 ASN A 31 SER A 36 5 6 HELIX 2 2 ASN A 50 GLN A 56 1 7 HELIX 3 3 LEU A 62 MET A 70 1 9 HELIX 4 4 ALA A 79 HIS A 83 5 5 HELIX 5 5 TYR A 84 GLY A 97 1 14 HELIX 6 6 GLY A 111 PHE A 115 5 5 HELIX 7 7 PRO A 117 THR A 125 5 9 HELIX 8 8 ASN A 126 LEU A 134 1 9 HELIX 9 9 LEU A 134 GLY A 142 1 9 HELIX 10 10 ASN A 143 LEU A 145 5 3 HELIX 11 11 SER A 146 MET A 162 1 17 HELIX 12 12 GLY A 226 ASN A 230 5 5 HELIX 13 13 ASP A 232 ARG A 246 1 15 HELIX 14 14 ASN A 250 THR A 263 1 14 HELIX 15 15 GLU A 279 ALA A 283 5 5 HELIX 16 16 ASP A 284 GLN A 288 5 5 HELIX 17 17 ILE A 300 ALA A 304 5 5 HELIX 18 18 ARG A 352 LEU A 356 5 5 HELIX 19 19 THR A 372 ASP A 381 1 10 HELIX 20 20 ASP A 381 ASP A 394 1 14 HELIX 21 21 ASP A 394 ARG A 412 1 19 HELIX 22 22 PRO A 416 TYR A 420 5 5 HELIX 23 23 LEU A 430 ASP A 434 5 5 HELIX 24 24 ASP A 444 SER A 455 1 12 HELIX 25 25 SER A 458 ARG A 471 1 14 HELIX 26 26 ALA A 482 LEU A 489 5 8 HELIX 27 27 PRO A 491 GLU A 499 5 9 HELIX 28 28 ASP A 501 THR A 517 1 17 HELIX 29 29 THR A 520 ALA A 540 1 21 HELIX 30 30 PHE A 565 GLU A 569 5 5 HELIX 31 31 ALA A 574 THR A 577 5 4 HELIX 32 32 ARG A 586 GLY A 599 1 14 HELIX 33 33 THR A 601 LEU A 615 1 15 HELIX 34 34 ASN A 618 THR A 622 5 5 HELIX 35 35 ASN A 636 THR A 643 1 8 HELIX 36 36 THR A 672 VAL A 677 1 6 HELIX 37 37 PHE A 678 SER A 680 5 3 HELIX 38 38 ASN A 681 ALA A 692 1 12 HELIX 39 39 ASN A 696 ASN A 713 1 18 SHEET 1 A 2 TYR A 202 THR A 203 0 SHEET 2 A 2 GLU A 207 LEU A 208 -1 O GLU A 207 N THR A 203 SHEET 1 B 2 TRP A 334 LYS A 338 0 SHEET 2 B 2 TRP A 344 PRO A 348 -1 O GLN A 345 N LYS A 337 SHEET 1 C 2 HIS A 572 ASP A 573 0 SHEET 2 C 2 GLY A 578 SER A 579 -1 O GLY A 578 N ASP A 573 SHEET 1 D 3 TYR A 647 PRO A 651 0 SHEET 2 D 3 TYR A 657 ASP A 661 -1 O CYS A 660 N LEU A 648 SHEET 3 D 3 VAL A 667 ALA A 671 -1 O TRP A 669 N ILE A 659 LINK CH2 TRP A 93 CE1 TYR A 221 1555 1555 1.56 LINK CE2 TYR A 221 SD MET A 247 1555 1555 1.82 LINK NE2 HIS A 262 FE HEM A 721 1555 1555 2.20 CISPEP 1 ALA A 116 PRO A 117 0 -0.22 CISPEP 2 ALA A 490 PRO A 491 0 0.05 SITE 1 AC1 23 GLY A 86 LEU A 87 ILE A 89 ARG A 90 SITE 2 AC1 23 TRP A 93 PRO A 224 LEU A 257 THR A 258 SITE 3 AC1 23 GLY A 261 HIS A 262 GLY A 265 LYS A 266 SITE 4 AC1 23 CYS A 267 HIS A 268 THR A 306 SER A 307 SITE 5 AC1 23 TRP A 313 ALA A 374 PHE A 402 TRP A 406 SITE 6 AC1 23 HOH A 742 HOH A 743 HOH A 769 CRYST1 109.208 109.208 202.661 90.00 90.00 90.00 P 41 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 0.009157 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009157 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004934 0.00000