HEADER OXIDOREDUCTASE 26-OCT-12 2YOR TITLE CRYSTALLIZATION OF A 45 KDA PEROXYGENASE- PEROXIDASE FROM THE MUSHROOM TITLE 2 AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY SAD UTILIZING ONLY TITLE 3 THE HAEM IRON CAVEAT 2YOR NAG J 1 HAS WRONG CHIRALITY AT ATOM C1 NAG B 401 C1 IS CAVEAT 2 2YOR PLANAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: AROMATIC PEROXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 47-371; COMPND 5 SYNONYM: AAPIIPH85, AAP; COMPND 6 EC: 1.11.2.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROCYBE AEGERITA; SOURCE 3 ORGANISM_COMMON: BLACK POPLAR MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5400; SOURCE 5 STRAIN: TM-A1; SOURCE 6 OTHER_DETAILS: GERMAN COLLECTION OF MICROORGANISMS (DSM), ACCESS SOURCE 7 NUMBER DSMZ 22459 KEYWDS OXIDOREDUCTASE, PEROXIDASE/PEROXYGENASE, UNSPECIFIC/AROMATIC KEYWDS 2 PEROXYGENASE, HEME, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.PIONTEK,E.STRITTMATTER,R.ULLRICH,D.A.PLATTNER,M.HOFRICHTER REVDAT 4 29-JUL-20 2YOR 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 01-APR-15 2YOR 1 JRNL REVDAT 2 11-DEC-13 2YOR 1 JRNL REVDAT 1 23-OCT-13 2YOR 0 JRNL AUTH K.PIONTEK,E.STRITTMATTER,R.ULLRICH,G.GROBE,M.J.PECYNA, JRNL AUTH 2 M.KLUGE,K.SCHEIBNER,M.HOFRICHTER,D.A.PLATTNER JRNL TITL STRUCTURAL BASIS OF SUBSTRATE CONVERSION IN A NEW AROMATIC JRNL TITL 2 PEROXYGENASE: P450 FUNCTIONALITY WITH BENEFITS JRNL REF J.BIOL.CHEM. V. 288 34767 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24126915 JRNL DOI 10.1074/JBC.M113.514521 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.PIONTEK,R.ULLRICH,C.LIERS,K.DIEDERICHS,D.A.PLATTNER, REMARK 1 AUTH 2 M.HOFRICHTER REMARK 1 TITL CRYSTALLIZATION OF A 45 KDA PEROXYGENASE/PEROXIDASE FROM THE REMARK 1 TITL 2 MUSHROOM AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY REMARK 1 TITL 3 SAD UTILIZING ONLY THE HAEM IRON. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 66 693 2010 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 20516602 REMARK 1 DOI 10.1107/S1744309110013515 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45282 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2384 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2896 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.4500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5025 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 584 REMARK 3 SOLVENT ATOMS : 643 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : -1.01000 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): 0.210 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.838 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5802 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7959 ; 1.617 ; 2.094 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 650 ; 7.323 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 262 ;33.608 ;23.817 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 754 ;15.619 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;18.751 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 903 ; 0.140 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4429 ; 0.020 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3245 ; 2.904 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5237 ; 4.239 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2557 ; 3.654 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2720 ; 5.219 ; 3.000 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 2YOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290054594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 47.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.77 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD, SHELXE, AUTOSHARP, SOLOMON REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, 100MM TRIS-HCL REMARK 280 PH 8.5 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 38.64500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.60000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.51500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.60000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.64500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.51500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -98.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 LEU A 4 REMARK 465 ASP B 328 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 ND2 ASN A 286 O5 NAG A 391 2.02 REMARK 500 O HOH B 2074 O HOH B 2253 2.03 REMARK 500 O HOH B 2271 O HOH B 2272 2.08 REMARK 500 O3 SO4 B 1357 O HOH B 2291 2.10 REMARK 500 O HOH A 2119 O HOH A 2261 2.10 REMARK 500 O HOH B 2023 O HOH B 2052 2.16 REMARK 500 O1 BMA A 501 O HOH A 2297 2.18 REMARK 500 O HOH B 2053 O HOH B 2054 2.19 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 B 100 NE - CZ - NH1 ANGL. DEV. = -3.4 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 ASP A 91 34.47 74.82 REMARK 500 VAL A 112 55.87 39.36 REMARK 500 THR A 120 -72.05 -84.79 REMARK 500 PHE A 185 55.29 -149.36 REMARK 500 ASP A 187 -124.53 53.54 REMARK 500 SER A 240 -89.63 -143.44 REMARK 500 CYS A 319 176.72 68.69 REMARK 500 ASN B 11 95.57 41.31 REMARK 500 ASP B 19 -169.83 -103.57 REMARK 500 PRO B 29 132.90 -16.78 REMARK 500 ASP B 91 39.97 71.50 REMARK 500 ASP B 187 -125.74 49.96 REMARK 500 SER B 240 -93.54 -142.79 REMARK 500 VAL B 259 71.42 -113.80 REMARK 500 ILE B 287 -61.34 -109.03 REMARK 500 THR B 297 174.25 -59.44 REMARK 500 CYS B 319 175.25 68.03 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 PRO B 29 GLY B 30 -147.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2063 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A2347 DISTANCE = 7.81 ANGSTROMS REMARK 525 HOH A2348 DISTANCE = 9.40 ANGSTROMS REMARK 525 HOH A2349 DISTANCE = 7.25 ANGSTROMS REMARK 525 HOH A2350 DISTANCE = 7.35 ANGSTROMS REMARK 525 HOH B2048 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B2293 DISTANCE = 6.03 ANGSTROMS 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 350 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 HEM A 350 NA 97.3 REMARK 620 3 HEM A 350 NB 93.2 87.5 REMARK 620 4 HEM A 350 NC 85.4 177.2 91.6 REMARK 620 5 HEM A 350 ND 90.6 91.0 176.1 89.7 REMARK 620 6 MZ0 A 354 N3 172.6 85.9 80.3 91.3 96.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 353 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 122 OE2 REMARK 620 2 GLY A 123 O 82.1 REMARK 620 3 SER A 126 OG 170.5 96.2 REMARK 620 4 HEM A 350 O1A 98.4 90.2 90.9 REMARK 620 5 HOH A2151 O 83.0 87.1 87.6 176.7 REMARK 620 6 HOH A2152 O 88.3 170.1 93.0 93.3 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 350 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 36 SG REMARK 620 2 HEM B 350 NA 94.8 REMARK 620 3 HEM B 350 NB 93.3 89.0 REMARK 620 4 HEM B 350 NC 87.0 178.1 91.4 REMARK 620 5 HEM B 350 ND 90.0 89.8 176.6 89.7 REMARK 620 6 MZ0 B 354 N3 167.0 91.9 75.7 86.4 101.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 353 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 122 OE2 REMARK 620 2 GLY B 123 O 78.8 REMARK 620 3 SER B 126 OG 171.9 100.3 REMARK 620 4 HEM B 350 O1A 96.5 89.1 91.6 REMARK 620 5 HOH B2125 O 78.8 88.1 93.2 174.9 REMARK 620 6 HOH B2126 O 90.1 168.6 91.0 89.5 92.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YP1 RELATED DB: PDB REMARK 900 CRYSTALLIZATION OF A 45 KDA PEROXYGENASE- PEROXIDASE FROM THE REMARK 900 MUSHROOM AGROCYBE AEGERITA AND STRUCTURE DETERMINATION BY SAD REMARK 900 UTILIZING ONLY THE HAEM IRON REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE MATURE PROTEIN BEGINS AT E44 WITH RESPECT TO B9W4V6. REMARK 999 CRYSTALLIZED PROTEIN BEGINS AT L47, THAT IS L4 IN THE REMARK 999 COORDINATE FILE, DUE TO PROTEOLYTIC CLEAVAGE. DBREF 2YOR A 4 328 UNP B9W4V6 APO1_AGRAE 47 371 DBREF 2YOR B 4 328 UNP B9W4V6 APO1_AGRAE 47 371 SEQRES 1 A 325 LEU PRO PRO GLY PRO LEU GLU ASN SER SER ALA LYS LEU SEQRES 2 A 325 VAL ASN ASP GLU ALA HIS PRO TRP LYS PRO LEU ARG PRO SEQRES 3 A 325 GLY ASP ILE ARG GLY PRO CYS PRO GLY LEU ASN THR LEU SEQRES 4 A 325 ALA SER HIS GLY TYR LEU PRO ARG ASN GLY VAL ALA THR SEQRES 5 A 325 PRO VAL GLN ILE ILE ASN ALA VAL GLN GLU GLY LEU ASN SEQRES 6 A 325 PHE ASP ASN GLN ALA ALA VAL PHE ALA THR TYR ALA ALA SEQRES 7 A 325 HIS LEU VAL ASP GLY ASN LEU ILE THR ASP LEU LEU SER SEQRES 8 A 325 ILE GLY ARG LYS THR ARG LEU THR GLY PRO ASP PRO PRO SEQRES 9 A 325 PRO PRO ALA SER VAL GLY GLY LEU ASN GLU HIS GLY THR SEQRES 10 A 325 PHE GLU GLY ASP ALA SER MET THR ARG GLY ASP ALA PHE SEQRES 11 A 325 PHE GLY ASN ASN HIS ASP PHE ASN GLU THR LEU PHE GLU SEQRES 12 A 325 GLN LEU VAL ASP TYR SER ASN ARG PHE GLY GLY GLY LYS SEQRES 13 A 325 TYR ASN LEU THR VAL ALA GLY GLU LEU ARG PHE LYS ARG SEQRES 14 A 325 ILE GLN ASP SER ILE ALA THR ASN PRO ASN PHE SER PHE SEQRES 15 A 325 VAL ASP PHE ARG PHE PHE THR ALA TYR GLY GLU THR THR SEQRES 16 A 325 PHE PRO ALA ASN LEU PHE VAL ASP GLY ARG ARG ASP ASP SEQRES 17 A 325 GLY GLN LEU ASP MET ASP ALA ALA ARG SER PHE PHE GLN SEQRES 18 A 325 PHE SER ARG MET PRO ASP ASP PHE PHE ARG ALA PRO SER SEQRES 19 A 325 PRO ARG SER GLY THR GLY VAL GLU VAL VAL ILE GLN ALA SEQRES 20 A 325 HIS PRO MET GLN PRO GLY ARG ASN VAL GLY LYS ILE ASN SEQRES 21 A 325 SER TYR THR VAL ASP PRO THR SER SER ASP PHE SER THR SEQRES 22 A 325 PRO CYS LEU MET TYR GLU LYS PHE VAL ASN ILE THR VAL SEQRES 23 A 325 LYS SER LEU TYR PRO ASN PRO THR VAL GLN LEU ARG LYS SEQRES 24 A 325 ALA LEU ASN THR ASN LEU ASP PHE PHE PHE GLN GLY VAL SEQRES 25 A 325 ALA ALA GLY CYS THR GLN VAL PHE PRO TYR GLY ARG ASP SEQRES 1 B 325 LEU PRO PRO GLY PRO LEU GLU ASN SER SER ALA LYS LEU SEQRES 2 B 325 VAL ASN ASP GLU ALA HIS PRO TRP LYS PRO LEU ARG PRO SEQRES 3 B 325 GLY ASP ILE ARG GLY PRO CYS PRO GLY LEU ASN THR LEU SEQRES 4 B 325 ALA SER HIS GLY TYR LEU PRO ARG ASN GLY VAL ALA THR SEQRES 5 B 325 PRO VAL GLN ILE ILE ASN ALA VAL GLN GLU GLY LEU ASN SEQRES 6 B 325 PHE ASP ASN GLN ALA ALA VAL PHE ALA THR TYR ALA ALA SEQRES 7 B 325 HIS LEU VAL ASP GLY ASN LEU ILE THR ASP LEU LEU SER SEQRES 8 B 325 ILE GLY ARG LYS THR ARG LEU THR GLY PRO ASP PRO PRO SEQRES 9 B 325 PRO PRO ALA SER VAL GLY GLY LEU ASN GLU HIS GLY THR SEQRES 10 B 325 PHE GLU GLY ASP ALA SER MET THR ARG GLY ASP ALA PHE SEQRES 11 B 325 PHE GLY ASN ASN HIS ASP PHE ASN GLU THR LEU PHE GLU SEQRES 12 B 325 GLN LEU VAL ASP TYR SER ASN ARG PHE GLY GLY GLY LYS SEQRES 13 B 325 TYR ASN LEU THR VAL ALA GLY GLU LEU ARG PHE LYS ARG SEQRES 14 B 325 ILE GLN ASP SER ILE ALA THR ASN PRO ASN PHE SER PHE SEQRES 15 B 325 VAL ASP PHE ARG PHE PHE THR ALA TYR GLY GLU THR THR SEQRES 16 B 325 PHE PRO ALA ASN LEU PHE VAL ASP GLY ARG ARG ASP ASP SEQRES 17 B 325 GLY GLN LEU ASP MET ASP ALA ALA ARG SER PHE PHE GLN SEQRES 18 B 325 PHE SER ARG MET PRO ASP ASP PHE PHE ARG ALA PRO SER SEQRES 19 B 325 PRO ARG SER GLY THR GLY VAL GLU VAL VAL ILE GLN ALA SEQRES 20 B 325 HIS PRO MET GLN PRO GLY ARG ASN VAL GLY LYS ILE ASN SEQRES 21 B 325 SER TYR THR VAL ASP PRO THR SER SER ASP PHE SER THR SEQRES 22 B 325 PRO CYS LEU MET TYR GLU LYS PHE VAL ASN ILE THR VAL SEQRES 23 B 325 LYS SER LEU TYR PRO ASN PRO THR VAL GLN LEU ARG LYS SEQRES 24 B 325 ALA LEU ASN THR ASN LEU ASP PHE PHE PHE GLN GLY VAL SEQRES 25 B 325 ALA ALA GLY CYS THR GLN VAL PHE PRO TYR GLY ARG ASP MODRES 2YOR ASN A 11 ASN GLYCOSYLATION SITE MODRES 2YOR ASN A 141 ASN GLYCOSYLATION SITE MODRES 2YOR ASN A 161 ASN GLYCOSYLATION SITE MODRES 2YOR ASN A 182 ASN GLYCOSYLATION SITE MODRES 2YOR ASN A 286 ASN GLYCOSYLATION SITE MODRES 2YOR ASN A 295 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 11 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 141 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 161 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 182 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 286 ASN GLYCOSYLATION SITE MODRES 2YOR ASN B 295 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET MAN F 4 11 HET MAN F 5 11 HET MAN F 6 11 HET MAN F 7 11 HET MAN F 8 11 HET NAG G 1 14 HET NAG G 2 14 HET NAG H 1 14 HET NAG H 2 14 HET NAG I 1 14 HET NAG I 2 14 HET NAG J 1 14 HET NAG J 2 14 HET HEM A 350 43 HET MG A 353 1 HET MZ0 A 354 7 HET NAG A 391 14 HET NAG A 401 14 HET NAG A 411 14 HET BMA A 501 12 HET SO4 A1355 5 HET CL A1356 1 HET SO4 A1357 5 HET SO4 A1358 5 HET HEM B 350 43 HET MG B 353 1 HET MZ0 B 354 7 HET NAG B 411 14 HET BMA B 501 12 HET NAG B 511 15 HET TRS B1355 8 HET CL B1356 1 HET SO4 B1357 5 HET CL B1358 1 HET SO4 B1359 5 HET SO4 B1360 5 HET CL B1361 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MG MAGNESIUM ION HETNAM MZ0 1H-IMIDAZOL-5-YLMETHANOL HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN HEM HEME HETSYN MZ0 4(5)-(HYDROXYMETHYL)IMIDAZOLE HETSYN TRS TRIS BUFFER FORMUL 3 NAG 21(C8 H15 N O6) FORMUL 3 BMA 6(C6 H12 O6) FORMUL 4 MAN 7(C6 H12 O6) FORMUL 11 HEM 2(C34 H32 FE N4 O4) FORMUL 12 MG 2(MG 2+) FORMUL 13 MZ0 2(C4 H6 N2 O) FORMUL 18 SO4 6(O4 S 2-) FORMUL 19 CL 4(CL 1-) FORMUL 28 TRS C4 H12 N O3 1+ FORMUL 35 HOH *643(H2 O) HELIX 1 1 CYS A 36 HIS A 45 1 10 HELIX 2 2 THR A 55 ASN A 68 1 14 HELIX 3 3 ASP A 70 GLY A 86 1 17 HELIX 4 4 THR A 99 GLY A 103 5 5 HELIX 5 5 ASP A 131 GLY A 135 5 5 HELIX 6 6 ASN A 141 GLY A 156 1 16 HELIX 7 7 ASN A 161 ASN A 180 1 20 HELIX 8 8 VAL A 186 THR A 197 1 12 HELIX 9 9 THR A 198 PHE A 204 1 7 HELIX 10 10 ASP A 215 SER A 226 1 12 HELIX 11 11 GLY A 243 HIS A 251 1 9 HELIX 12 12 THR A 276 ILE A 287 1 12 HELIX 13 13 ILE A 287 TYR A 293 1 7 HELIX 14 14 THR A 297 GLY A 314 1 18 HELIX 15 15 CYS B 36 HIS B 45 1 10 HELIX 16 16 THR B 55 ASN B 68 1 14 HELIX 17 17 ASP B 70 GLY B 86 1 17 HELIX 18 18 THR B 99 GLY B 103 5 5 HELIX 19 19 ASP B 131 GLY B 135 5 5 HELIX 20 20 ASN B 141 GLY B 156 1 16 HELIX 21 21 ASN B 161 ASN B 180 1 20 HELIX 22 22 VAL B 186 PHE B 204 1 19 HELIX 23 23 ASP B 215 PHE B 225 1 11 HELIX 24 24 GLY B 243 HIS B 251 1 9 HELIX 25 25 THR B 276 ILE B 287 1 12 HELIX 26 26 ILE B 287 TYR B 293 1 7 HELIX 27 27 THR B 297 GLY B 314 1 18 SHEET 1 AA 2 VAL A 53 ALA A 54 0 SHEET 2 AA 2 LEU A 93 SER A 94 -1 O LEU A 93 N ALA A 54 SHEET 1 AB 3 SER A 184 PHE A 185 0 SHEET 2 AB 3 GLY A 256 ARG A 257 -1 O GLY A 256 N PHE A 185 SHEET 3 AB 3 THR A 266 VAL A 267 -1 O THR A 266 N ARG A 257 SHEET 1 BA 2 VAL B 53 ALA B 54 0 SHEET 2 BA 2 LEU B 93 SER B 94 -1 O LEU B 93 N ALA B 54 SHEET 1 BB 3 SER B 184 PHE B 185 0 SHEET 2 BB 3 GLY B 256 ARG B 257 -1 O GLY B 256 N PHE B 185 SHEET 3 BB 3 THR B 266 VAL B 267 -1 O THR B 266 N ARG B 257 SSBOND 1 CYS A 278 CYS A 319 1555 1555 2.06 SSBOND 2 CYS B 278 CYS B 319 1555 1555 2.07 LINK ND2 ASN A 11 C1 NAG A 411 1555 1555 1.45 LINK ND2 ASN A 141 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 161 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 182 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 286 C1 NAG A 391 1555 1555 1.48 LINK ND2 ASN A 295 C1 NAG A 401 1555 1555 1.45 LINK ND2 ASN B 11 C1 NAG B 411 1555 1555 1.44 LINK ND2 ASN B 141 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN B 161 C1 NAG G 1 1555 1555 1.44 LINK ND2 ASN B 182 C1 NAG H 1 1555 1555 1.44 LINK ND2 ASN B 286 C1 NAG I 1 1555 1555 1.45 LINK ND2 ASN B 295 C1 NAG J 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.45 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.43 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.43 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44 LINK O6 BMA F 3 C1 MAN F 4 1555 1555 1.44 LINK O3 BMA F 3 C1 MAN F 8 1555 1555 1.45 LINK O6 MAN F 4 C1 MAN F 5 1555 1555 1.44 LINK O3 MAN F 4 C1 MAN F 7 1555 1555 1.44 LINK O2 MAN F 5 C1 MAN F 6 1555 1555 1.45 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.41 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.46 LINK O4 NAG I 1 C1 NAG I 2 1555 1555 1.44 LINK O4 NAG J 1 C1 NAG J 2 1555 1555 1.45 LINK SG CYS A 36 FE HEM A 350 1555 1555 2.29 LINK OE2 GLU A 122 MG MG A 353 1555 1555 1.95 LINK O GLY A 123 MG MG A 353 1555 1555 2.16 LINK OG SER A 126 MG MG A 353 1555 1555 2.08 LINK O1A HEM A 350 MG MG A 353 1555 1555 2.10 LINK FE HEM A 350 N3 MZ0 A 354 1555 1555 2.36 LINK MG MG A 353 O HOH A2151 1555 1555 1.87 LINK MG MG A 353 O HOH A2152 1555 1555 2.13 LINK SG CYS B 36 FE HEM B 350 1555 1555 2.36 LINK OE2 GLU B 122 MG MG B 353 1555 1555 2.12 LINK O GLY B 123 MG MG B 353 1555 1555 2.18 LINK OG SER B 126 MG MG B 353 1555 1555 2.09 LINK O1A HEM B 350 MG MG B 353 1555 1555 2.06 LINK FE HEM B 350 N3 MZ0 B 354 1555 1555 2.34 LINK MG MG B 353 O HOH B2125 1555 1555 2.15 LINK MG MG B 353 O HOH B2126 1555 1555 2.22 CISPEP 1 PRO A 108 PRO A 109 0 11.37 CISPEP 2 PRO B 108 PRO B 109 0 5.22 CRYST1 77.290 95.030 127.200 90.00 90.00 90.00 P 21 21 21 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 0.012938 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007862 0.00000 MTRIX1 1 0.039960 -0.994150 0.100330 1.86543 1 MTRIX2 1 -0.995330 -0.048430 -0.083480 27.07028 1 MTRIX3 1 0.087850 -0.096530 -0.991450 268.24673 1