HEADER OXIDOREDUCTASE 15-MAR-02 1GWH TITLE ATOMIC RESOLUTION STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE TITLE 2 COMPLEXED WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.11.1.6 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROCOCCUS LUTEUS; SOURCE 3 ORGANISM_COMMON: MICROCOCCUS LYSODEIKTICUS; SOURCE 4 ORGANISM_TAXID: 1270 KEYWDS OXIDOREDUCTASE, CATALASE, HYDROGEN PEROXIDE OXIDOREDUCTASE, KEYWDS 2 PEROXIDASE EXPDTA X-RAY DIFFRACTION AUTHOR G.N.MURSHUDOV,A.I.GREBENKO,J.A.BRANNIGAN,A.A.ANTSON,V.V.BARYNIN, AUTHOR 2 G.G.DODSON,Z.DAUTER,K.S.WILSON,W.R.MELIK-ADAMYAN REVDAT 8 24-JUL-19 1GWH 1 REMARK REVDAT 7 10-JUL-19 1GWH 1 REMARK REVDAT 6 19-DEC-18 1GWH 1 JRNL REMARK LINK REVDAT 5 20-JUN-18 1GWH 1 COMPND SOURCE JRNL REMARK REVDAT 5 2 1 DBREF SEQADV REVDAT 4 15-APR-15 1GWH 1 JRNL REMARK VERSN FORMUL REVDAT 3 24-FEB-09 1GWH 1 VERSN REVDAT 2 05-DEC-02 1GWH 1 JRNL REVDAT 1 19-MAR-02 1GWH 0 JRNL AUTH G.N.MURSHUDOV,A.I.GREBENKO,J.A.BRANNIGAN,A.A.ANTSON, JRNL AUTH 2 V.V.BARYNIN,G.G.DODSON,Z.DAUTER,K.S.WILSON,W.R.MELIK-ADAMYAN JRNL TITL THE STRUCTURES OF MICROCOCCUS LYSODEIKTICUS CATALASE, ITS JRNL TITL 2 FERRYL INTERMEDIATE (COMPOUND II) AND NADPH COMPLEX. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 1972 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 12454454 JRNL DOI 10.1107/S0907444902016566 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.11 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 52087 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.111 REMARK 3 FREE R VALUE : 0.138 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2758 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.79 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1756 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3981 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 103 REMARK 3 SOLVENT ATOMS : 568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.078 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.497 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4260 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3614 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 5807 ; 1.563 ; 1.958 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 8409 ; 0.948 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 589 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4824 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 912 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 754 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4103 ; 0.264 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2226 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 355 ; 0.181 ; 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): 21 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 233 ; 0.331 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 67 ; 0.172 ; 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): 2492 ; 0.849 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4028 ; 1.574 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1768 ; 2.685 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1779 ; 4.403 ; 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 : BABINET MODEL PLUS 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 1GWH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-02. REMARK 100 THE DEPOSITION ID IS D_1290009574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-94 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 5.20 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 457407 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.744 REMARK 200 RESOLUTION RANGE LOW (A) : 74.536 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.20 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 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 0.000000 -1.000000 0.000000 53.35000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 53.12500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.35000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.35000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.12500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.35000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.12500 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 1 REMARK 465 GLU A 2 REMARK 465 HIS A 3 REMARK 465 GLN A 4 REMARK 465 LYS A 5 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 NE2 GLN A 290 O7N NDP A 505 1.03 REMARK 500 CD GLN A 290 O7N NDP A 505 1.40 REMARK 500 NE2 GLN A 290 C7N NDP A 505 1.58 REMARK 500 OE1 GLN A 290 O7N NDP A 505 1.67 REMARK 500 CD GLN A 290 C7N NDP A 505 1.69 REMARK 500 OE1 GLN A 290 C7N NDP A 505 1.88 REMARK 500 OE1 GLN A 290 N7N NDP A 505 1.95 REMARK 500 O HOH A 2377 O HOH A 2380 2.07 REMARK 500 NE2 GLN A 290 C4N NDP A 505 2.10 REMARK 500 NE2 HIS A 487 O HOH A 2530 2.13 REMARK 500 NE2 GLN A 290 C3N NDP A 505 2.14 REMARK 500 OD1 ASP A 169 NH2 ARG A 464 2.15 REMARK 500 OD1 ASP A 440 O HOH A 2475 2.15 REMARK 500 NZ LYS A 291 O3D NDP A 505 2.16 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 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 292 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 464 CG - CD - NE ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG A 464 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 464 NE - CZ - NH2 ANGL. DEV. = -3.9 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 VAL A 22 -53.85 77.80 REMARK 500 HIS A 61 34.93 71.14 REMARK 500 LYS A 154 -127.04 -105.48 REMARK 500 SER A 202 -62.91 71.84 REMARK 500 PRO A 332 11.62 -66.04 REMARK 500 HIS A 354 32.11 -99.30 REMARK 500 GLU A 373 -160.40 66.37 REMARK 500 ASP A 398 52.12 -157.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NDP A 505 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 2563 REMARK 615 NDP A 505 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 504 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 343 OH REMARK 620 2 HEM A 504 NA 97.9 REMARK 620 3 HEM A 504 NB 97.8 87.8 REMARK 620 4 HEM A 504 NC 94.5 167.6 90.0 REMARK 620 5 HEM A 504 ND 92.7 90.1 169.4 89.9 REMARK 620 6 HOH A2566 O 174.6 84.9 86.9 82.8 82.6 REMARK 620 7 ACT A 507 O 166.6 94.9 86.5 72.8 83.3 10.1 REMARK 620 N 1 2 3 4 5 6 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: Binding site for residues NDP A 505 and SO4 A REMARK 800 506 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GWE RELATED DB: PDB REMARK 900 ATOMIC RESOLUTION STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE REMARK 900 AND ITS FERRYL INTERMEDIATE REMARK 900 RELATED ID: 1GWF RELATED DB: PDB REMARK 900 COMPOUND II STRUCTURE OF MICROCOCCUS LYSODEIKTICUS CATALASE DBREF 1GWH A 1 503 UNP P29422 CATA_MICLU 1 503 SEQADV 1GWH ILE A 503 UNP P29422 MET 503 CONFLICT SEQRES 1 A 503 MET GLU HIS GLN LYS THR THR PRO HIS ALA THR GLY SER SEQRES 2 A 503 THR ARG GLN ASN GLY ALA PRO ALA VAL SER ASP ARG GLN SEQRES 3 A 503 SER LEU THR VAL GLY SER GLU GLY PRO ILE VAL LEU HIS SEQRES 4 A 503 ASP THR HIS LEU LEU GLU THR HIS GLN HIS PHE ASN ARG SEQRES 5 A 503 MET ASN ILE PRO GLU ARG ARG PRO HIS ALA LYS GLY SER SEQRES 6 A 503 GLY ALA PHE GLY GLU PHE GLU VAL THR GLU ASP VAL SER SEQRES 7 A 503 LYS TYR THR LYS ALA LEU VAL PHE GLN PRO GLY THR LYS SEQRES 8 A 503 THR GLU THR LEU LEU ARG PHE SER THR VAL ALA GLY GLU SEQRES 9 A 503 LEU GLY SER PRO ASP THR TRP ARG ASP VAL ARG GLY PHE SEQRES 10 A 503 ALA LEU ARG PHE TYR THR GLU GLU GLY ASN TYR ASP LEU SEQRES 11 A 503 VAL GLY ASN ASN THR PRO ILE PHE PHE LEU ARG ASP PRO SEQRES 12 A 503 MET LYS PHE THR HIS PHE ILE ARG SER GLN LYS ARG LEU SEQRES 13 A 503 PRO ASP SER GLY LEU ARG ASP ALA THR MET GLN TRP ASP SEQRES 14 A 503 PHE TRP THR ASN ASN PRO GLU SER ALA HIS GLN VAL THR SEQRES 15 A 503 TYR LEU MET GLY PRO ARG GLY LEU PRO ARG THR TRP ARG SEQRES 16 A 503 GLU MET ASN GLY TYR GLY SER HIS THR TYR LEU TRP VAL SEQRES 17 A 503 ASN ALA GLN GLY GLU LYS HIS TRP VAL LYS TYR HIS PHE SEQRES 18 A 503 ILE SER GLN GLN GLY VAL HIS ASN LEU SER ASN ASP GLU SEQRES 19 A 503 ALA THR LYS ILE ALA GLY GLU ASN ALA ASP PHE HIS ARG SEQRES 20 A 503 GLN ASP LEU PHE GLU SER ILE ALA LYS GLY ASP HIS PRO SEQRES 21 A 503 LYS TRP ASP LEU TYR ILE GLN ALA ILE PRO TYR GLU GLU SEQRES 22 A 503 GLY LYS THR TYR ARG PHE ASN PRO PHE ASP LEU THR LYS SEQRES 23 A 503 THR ILE SER GLN LYS ASP TYR PRO ARG ILE LYS VAL GLY SEQRES 24 A 503 THR LEU THR LEU ASN ARG ASN PRO GLU ASN HIS PHE ALA SEQRES 25 A 503 GLN ILE GLU SER ALA ALA PHE SER PRO SER ASN THR VAL SEQRES 26 A 503 PRO GLY ILE GLY LEU SER PRO ASP ARG MET LEU LEU GLY SEQRES 27 A 503 ARG ALA PHE ALA TYR HIS ASP ALA GLN LEU TYR ARG VAL SEQRES 28 A 503 GLY ALA HIS VAL ASN GLN LEU PRO VAL ASN ARG PRO LYS SEQRES 29 A 503 ASN ALA VAL HIS ASN TYR ALA PHE GLU GLY GLN MET TRP SEQRES 30 A 503 TYR ASP HIS THR GLY ASP ARG SER THR TYR VAL PRO ASN SEQRES 31 A 503 SER ASN GLY ASP SER TRP SER ASP GLU THR GLY PRO VAL SEQRES 32 A 503 ASP ASP GLY TRP GLU ALA ASP GLY THR LEU THR ARG GLU SEQRES 33 A 503 ALA GLN ALA LEU ARG ALA ASP ASP ASP ASP PHE GLY GLN SEQRES 34 A 503 ALA GLY THR LEU VAL ARG GLU VAL PHE SER ASP GLN GLU SEQRES 35 A 503 ARG ASP ASP PHE VAL GLU THR VAL ALA GLY ALA LEU LYS SEQRES 36 A 503 GLY VAL ARG GLN ASP VAL GLN ALA ARG ALA PHE GLU TYR SEQRES 37 A 503 TRP LYS ASN VAL ASP ALA THR ILE GLY GLN ARG ILE GLU SEQRES 38 A 503 ASP GLU VAL LYS ARG HIS GLU GLY ASP GLY ILE PRO GLY SEQRES 39 A 503 VAL GLU ALA GLY GLY GLU ALA ARG ILE HET HEM A 504 43 HET NDP A 505 47 HET SO4 A 506 5 HET ACT A 507 4 HET ACT A 508 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 SO4 O4 S 2- FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 7 HOH *568(H2 O) HELIX 1 1 ASP A 40 ASN A 51 1 12 HELIX 2 2 ALA A 83 GLN A 87 5 5 HELIX 3 3 ASP A 142 MET A 144 5 3 HELIX 4 4 LYS A 145 GLN A 153 1 9 HELIX 5 5 ASP A 163 ASN A 173 1 11 HELIX 6 6 ASN A 174 GLU A 176 5 3 HELIX 7 7 SER A 177 GLY A 186 1 10 HELIX 8 8 PRO A 187 LEU A 190 5 4 HELIX 9 9 THR A 193 MET A 197 5 5 HELIX 10 10 SER A 231 ASN A 242 1 12 HELIX 11 11 ASP A 244 LYS A 256 1 13 HELIX 12 12 GLU A 272 TYR A 277 1 6 HELIX 13 13 ASN A 309 ILE A 314 1 6 HELIX 14 14 ASP A 333 VAL A 351 1 19 HELIX 15 15 HIS A 354 LEU A 358 5 5 HELIX 16 16 LEU A 358 ARG A 362 5 5 HELIX 17 17 PHE A 427 VAL A 437 1 11 HELIX 18 18 SER A 439 LYS A 455 1 17 HELIX 19 19 ARG A 458 ASP A 473 1 16 HELIX 20 20 ASP A 473 ARG A 486 1 14 SHEET 1 AA12 GLY A 64 VAL A 73 0 SHEET 2 AA12 LYS A 91 SER A 99 -1 O THR A 92 N PHE A 71 SHEET 3 AA12 GLY A 116 THR A 123 -1 O GLY A 116 N SER A 99 SHEET 4 AA12 GLY A 126 ASN A 133 -1 O GLY A 126 N THR A 123 SHEET 5 AA12 GLY A 199 TYR A 200 -1 O TYR A 200 N ASN A 133 SHEET 6 AA12 LYS A 214 SER A 223 -1 O PHE A 221 N GLY A 199 SHEET 7 AA12 LYS A 261 PRO A 270 -1 O ASP A 263 N ILE A 222 SHEET 8 AA12 ILE A 296 ARG A 305 -1 O ILE A 296 N ILE A 266 SHEET 9 AA12 GLY A 64 VAL A 73 -1 O PHE A 68 N ASN A 304 SHEET 10 AA12 LYS A 91 SER A 99 -1 O THR A 92 N PHE A 71 SHEET 11 AA12 GLY A 116 THR A 123 -1 O GLY A 116 N SER A 99 SHEET 12 AA12 GLY A 64 VAL A 73 0 LINK OH TYR A 343 FE HEM A 504 1555 1555 1.91 LINK FE HEM A 504 O AHOH A2566 1555 1555 2.13 LINK FE HEM A 504 O ACT A 507 1555 1555 2.94 CISPEP 1 ARG A 59 PRO A 60 0 -9.32 CISPEP 2 VAL A 388 PRO A 389 0 -15.79 SITE 1 AC1 9 PRO A 60 HIS A 61 VAL A 101 ASN A 133 SITE 2 AC1 9 PHE A 138 PHE A 146 HEM A 504 HOH A2565 SITE 3 AC1 9 HOH A2566 SITE 1 AC2 8 VAL A 101 ASP A 113 VAL A 114 PHE A 139 SITE 2 AC2 8 PHE A 149 GLN A 153 HOH A2567 HOH A2568 SITE 1 AC3 26 HIS A 47 ASN A 51 ARG A 58 ARG A 59 SITE 2 AC3 26 HIS A 61 ARG A 97 GLY A 116 VAL A 131 SITE 3 AC3 26 GLY A 132 ASN A 133 PRO A 143 PHE A 146 SITE 4 AC3 26 GLY A 201 SER A 202 LEU A 284 PHE A 319 SITE 5 AC3 26 MET A 335 ARG A 339 TYR A 343 GLN A 347 SITE 6 AC3 26 ARG A 350 ACT A 507 HOH A2107 HOH A2553 SITE 7 AC3 26 HOH A2554 HOH A2566 SITE 1 AC4 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC4 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC4 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC4 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC4 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 AC5 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC5 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC5 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC5 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC5 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 AC6 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC6 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC6 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC6 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC6 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 AC7 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC7 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC7 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC7 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC7 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 AC8 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC8 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC8 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC8 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC8 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 AC9 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 AC9 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 AC9 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 AC9 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 AC9 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 BC1 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 BC1 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 BC1 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 BC1 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 BC1 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 BC2 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 BC2 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 BC2 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 BC2 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 BC2 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 BC3 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 BC3 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 BC3 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 BC3 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 BC3 19 HOH A2559 HOH A2560 HOH A2564 SITE 1 BC4 19 TYR A 183 PRO A 187 ARG A 188 ASN A 198 SITE 2 BC4 19 TYR A 200 SER A 289 GLN A 290 ARG A 295 SITE 3 BC4 19 VAL A 437 HOH A2198 HOH A2293 HOH A2295 SITE 4 BC4 19 HOH A2484 HOH A2555 HOH A2556 HOH A2557 SITE 5 BC4 19 HOH A2559 HOH A2560 HOH A2564 CRYST1 106.700 106.700 106.250 90.00 90.00 90.00 P 42 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 0.009372 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009412 0.00000