HEADER OXIDOREDUCTASE 27-SEP-17 6EKX TITLE DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN TITLE 2 COMPLEX WITH 1-NAPHTHOL (I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AROMATIC PEROXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AAP, UNSPECIFIC PEROXYGENASE, UPO; COMPND 5 EC: 1.11.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROCYBE AEGERITA; SOURCE 3 ORGANISM_COMMON: BLACK POPLAR MUSHROOM; SOURCE 4 ORGANISM_TAXID: 5400; SOURCE 5 GENE: APO1; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PHAFFII CBS 7435; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 981350; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X-33; SOURCE 9 EXPRESSION_SYSTEM_ATCC_NUMBER: 76273; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAB KEYWDS DIRECTED EVOLUTION, PADAI, UNSPECIFIC PEROXYGENASE, UPO, HEME- KEYWDS 2 THIOLATE PEROXIDASE, AGROCYBE AEGERITA, 1-NAPHTHOL, 1-NAPHTHALENOL, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.RAMIREZ-ESCUDERO,J.SANZ-APARICIO REVDAT 6 23-OCT-24 6EKX 1 REMARK REVDAT 5 17-JAN-24 6EKX 1 REMARK HETSYN REVDAT 4 29-JUL-20 6EKX 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE REVDAT 3 03-APR-19 6EKX 1 JRNL REVDAT 2 19-DEC-18 6EKX 1 JRNL REVDAT 1 12-DEC-18 6EKX 0 JRNL AUTH M.RAMIREZ-ESCUDERO,P.MOLINA-ESPEJA,P.GOMEZ DE SANTOS, JRNL AUTH 2 M.HOFRICHTER,J.SANZ-APARICIO,M.ALCALDE JRNL TITL STRUCTURAL INSIGHTS INTO THE SUBSTRATE PROMISCUITY OF A JRNL TITL 2 LABORATORY-EVOLVED PEROXYGENASE. JRNL REF ACS CHEM.BIOL. V. 13 3259 2018 JRNL REFN ESSN 1554-8937 JRNL PMID 30376293 JRNL DOI 10.1021/ACSCHEMBIO.8B00500 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 118360 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 6134 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7931 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 394 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 206 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : -0.68000 REMARK 3 B33 (A**2) : 0.50000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.454 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2878 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2586 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3914 ; 1.351 ; 2.016 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5952 ; 0.961 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 344 ; 5.824 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 135 ;32.440 ;23.630 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 397 ;11.918 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.054 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3267 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 634 ; 0.009 ; 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): 1373 ; 0.515 ; 1.127 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1348 ; 0.516 ; 1.104 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1702 ; 0.925 ; 1.657 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1703 ; 0.924 ; 1.660 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1505 ; 0.723 ; 1.244 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1506 ; 0.723 ; 1.245 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2213 ; 1.175 ; 1.829 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3574 ; 3.985 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3575 ; 3.985 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 50 ;26.588 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 45 ; 3.343 ; 5.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6EKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200006562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : KB MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 0.72 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 124527 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: MOLREP 11.5.02 REMARK 200 STARTING MODEL: 5OXU REMARK 200 REMARK 200 REMARK: CLUSTER OF PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M SODIUM POTASSIUM PHOSPHATE PH REMARK 280 5.6, 3% MPD, SOAKING 100MM 1-NAPHTHOL, 20% METHANOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.89950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 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 GLU A 1 REMARK 465 PRO A 2 REMARK 465 GLY A 3 REMARK 465 ASP A 328 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ALA A 317 CB 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 OE1 GLU A 196 O HOH A 503 0.23 REMARK 500 CD GLU A 196 O HOH A 503 1.41 REMARK 500 FE HEM A 401 O HOH A 508 1.64 REMARK 500 C6 1NP A 413 O HOH A 508 2.02 REMARK 500 C2 1NP A 413 C5 1NP A 414 2.10 REMARK 500 O HOH A 607 O HOH A 678 2.15 REMARK 500 OG SER A 111 O HOH A 501 2.19 REMARK 500 N LEU A 4 O HOH A 502 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 THR A 270 OG1 - CB - CG2 ANGL. DEV. = -13.8 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 120 -66.02 -95.70 REMARK 500 ASN A 136 105.20 -161.10 REMARK 500 HIS A 138 -36.01 -132.31 REMARK 500 ASP A 187 -126.40 52.04 REMARK 500 SER A 240 -89.62 -131.46 REMARK 500 HIS A 251 74.76 -152.54 REMARK 500 VAL A 259 51.66 -116.00 REMARK 500 ILE A 287 -60.14 -107.82 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 HEM A 401 NA 94.7 REMARK 620 3 HEM A 401 NB 84.9 87.3 REMARK 620 4 HEM A 401 NC 86.4 173.6 86.5 REMARK 620 5 HEM A 401 ND 93.9 94.4 178.0 91.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 122 OE2 REMARK 620 2 GLY A 123 O 84.7 REMARK 620 3 SER A 126 OG 173.7 94.0 REMARK 620 4 HEM A 401 O1A 103.1 83.9 82.9 REMARK 620 5 HOH A 633 O 91.5 175.5 90.0 94.6 REMARK 620 6 HOH A 671 O 84.2 89.6 89.7 169.7 92.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YOR RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN, UPO REMARK 900 RELATED ID: 2YP1 RELATED DB: PDB REMARK 900 WILD TYPE PROTEIN, UPO REMARK 900 RELATED ID: 5OXU RELATED DB: PDB REMARK 900 UPO-PADAI REMARK 900 RELATED ID: 5OXT RELATED DB: PDB REMARK 900 UPO-PADAI IN COMPLEX WITH ACETATE REMARK 900 RELATED ID: 5OY1 RELATED DB: PDB REMARK 900 UPO-PADAI IN COMPLEX WITH DMSO REMARK 900 RELATED ID: 5OY2 RELATED DB: PDB REMARK 900 UPO-PADAI IN COMPLEX WITH DMP REMARK 900 RELATED ID: 6EKW RELATED DB: PDB REMARK 900 UPO-PADAI IN COMPLEX WITH NAPHTHALENE DBREF 6EKX A 1 328 UNP B9W4V6 APO1_AGRAE 44 371 SEQADV 6EKX ALA A 57 UNP B9W4V6 VAL 100 ENGINEERED MUTATION SEQADV 6EKX PHE A 67 UNP B9W4V6 LEU 110 ENGINEERED MUTATION SEQADV 6EKX ILE A 75 UNP B9W4V6 VAL 118 ENGINEERED MUTATION SEQADV 6EKX VAL A 248 UNP B9W4V6 ILE 291 ENGINEERED MUTATION SEQADV 6EKX LEU A 311 UNP B9W4V6 PHE 354 ENGINEERED MUTATION SEQRES 1 A 328 GLU PRO GLY LEU PRO PRO GLY PRO LEU GLU ASN SER SER SEQRES 2 A 328 ALA LYS LEU VAL ASN ASP GLU ALA HIS PRO TRP LYS PRO SEQRES 3 A 328 LEU ARG PRO GLY ASP ILE ARG GLY PRO CYS PRO GLY LEU SEQRES 4 A 328 ASN THR LEU ALA SER HIS GLY TYR LEU PRO ARG ASN GLY SEQRES 5 A 328 VAL ALA THR PRO ALA GLN ILE ILE ASN ALA VAL GLN GLU SEQRES 6 A 328 GLY PHE ASN PHE ASP ASN GLN ALA ALA ILE PHE ALA THR SEQRES 7 A 328 TYR ALA ALA HIS LEU VAL ASP GLY ASN LEU ILE THR ASP SEQRES 8 A 328 LEU LEU SER ILE GLY ARG LYS THR ARG LEU THR GLY PRO SEQRES 9 A 328 ASP PRO PRO PRO PRO ALA SER VAL GLY GLY LEU ASN GLU SEQRES 10 A 328 HIS GLY THR PHE GLU GLY ASP ALA SER MET THR ARG GLY SEQRES 11 A 328 ASP ALA PHE PHE GLY ASN ASN HIS ASP PHE ASN GLU THR SEQRES 12 A 328 LEU PHE GLU GLN LEU VAL ASP TYR SER ASN ARG PHE GLY SEQRES 13 A 328 GLY GLY LYS TYR ASN LEU THR VAL ALA GLY GLU LEU ARG SEQRES 14 A 328 PHE LYS ARG ILE GLN ASP SER ILE ALA THR ASN PRO ASN SEQRES 15 A 328 PHE SER PHE VAL ASP PHE ARG PHE PHE THR ALA TYR GLY SEQRES 16 A 328 GLU THR THR PHE PRO ALA ASN LEU PHE VAL ASP GLY ARG SEQRES 17 A 328 ARG ASP ASP GLY GLN LEU ASP MET ASP ALA ALA ARG SER SEQRES 18 A 328 PHE PHE GLN PHE SER ARG MET PRO ASP ASP PHE PHE ARG SEQRES 19 A 328 ALA PRO SER PRO ARG SER GLY THR GLY VAL GLU VAL VAL SEQRES 20 A 328 VAL GLN ALA HIS PRO MET GLN PRO GLY ARG ASN VAL GLY SEQRES 21 A 328 LYS ILE ASN SER TYR THR VAL ASP PRO THR SER SER ASP SEQRES 22 A 328 PHE SER THR PRO CYS LEU MET TYR GLU LYS PHE VAL ASN SEQRES 23 A 328 ILE THR VAL LYS SER LEU TYR PRO ASN PRO THR VAL GLN SEQRES 24 A 328 LEU ARG LYS ALA LEU ASN THR ASN LEU ASP PHE LEU PHE SEQRES 25 A 328 GLN GLY VAL ALA ALA GLY CYS THR GLN VAL PHE PRO TYR SEQRES 26 A 328 GLY ARG ASP HET HEM A 401 43 HET MG A 402 1 HET CL A 403 1 HET NAG A 404 14 HET NAG A 405 14 HET NAG A 406 14 HET NAG A 407 14 HET NAG A 408 14 HET PO4 A 409 5 HET GOL A 410 6 HET GOL A 411 6 HET GOL A 412 6 HET 1NP A 413 11 HET 1NP A 414 11 HET MOH A 415 2 HET MOH A 416 2 HET MOH A 417 2 HET MOH A 418 2 HET MOH A 419 2 HET MOH A 420 2 HET MOH A 421 4 HET MOH A 422 2 HET MOH A 423 2 HET MOH A 424 2 HET MOH A 425 2 HET MOH A 426 2 HET MOH A 427 2 HET MOH A 428 2 HET MOH A 429 2 HET MOH A 430 2 HET MOH A 431 2 HET MOH A 432 2 HET MOH A 433 2 HET MOH A 434 2 HET MOH A 435 2 HET MOH A 436 2 HET MOH A 437 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM 1NP 1-NAPHTHOL HETNAM MOH METHANOL HETSYN HEM HEME HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 1NP NAPHTHALEN-1-OL FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 MG MG 2+ FORMUL 4 CL CL 1- FORMUL 5 NAG 5(C8 H15 N O6) FORMUL 10 PO4 O4 P 3- FORMUL 11 GOL 3(C3 H8 O3) FORMUL 14 1NP 2(C10 H8 O) FORMUL 16 MOH 23(C H4 O) FORMUL 39 HOH *438(H2 O) HELIX 1 AA1 CYS A 36 HIS A 45 1 10 HELIX 2 AA2 THR A 55 ASN A 68 1 14 HELIX 3 AA3 ASP A 70 GLY A 86 1 17 HELIX 4 AA4 THR A 99 GLY A 103 5 5 HELIX 5 AA5 ASP A 131 GLY A 135 5 5 HELIX 6 AA6 ASN A 141 GLY A 156 1 16 HELIX 7 AA7 ASN A 161 ASN A 180 1 20 HELIX 8 AA8 VAL A 186 PHE A 204 1 19 HELIX 9 AA9 ASP A 215 SER A 226 1 12 HELIX 10 AB1 GLY A 243 HIS A 251 1 9 HELIX 11 AB2 THR A 276 ILE A 287 1 12 HELIX 12 AB3 ILE A 287 TYR A 293 1 7 HELIX 13 AB4 THR A 297 GLY A 314 1 18 SHEET 1 AA1 2 VAL A 53 ALA A 54 0 SHEET 2 AA1 2 LEU A 93 SER A 94 -1 O LEU A 93 N ALA A 54 SHEET 1 AA2 3 SER A 184 PHE A 185 0 SHEET 2 AA2 3 GLY A 256 ARG A 257 -1 O GLY A 256 N PHE A 185 SHEET 3 AA2 3 THR A 266 VAL A 267 -1 O THR A 266 N ARG A 257 SSBOND 1 CYS A 278 CYS A 319 1555 1555 2.06 LINK ND2 ASN A 11 C1 NAG A 404 1555 1555 1.36 LINK ND2 ASN A 141 C1 NAG A 406 1555 1555 1.38 LINK ND2 ASN A 161 C1 NAG A 407 1555 1555 1.35 LINK ND2 ASN A 182 C1 NAG A 408 1555 1555 1.39 LINK ND2 ASN A 286 C1 NAG A 405 1555 1555 1.39 LINK SG CYS A 36 FE HEM A 401 1555 1555 2.66 LINK OE2 GLU A 122 MG MG A 402 1555 1555 2.07 LINK O GLY A 123 MG MG A 402 1555 1555 2.11 LINK OG SER A 126 MG MG A 402 1555 1555 2.13 LINK O1A HEM A 401 MG MG A 402 1555 1555 2.28 LINK MG MG A 402 O HOH A 633 1555 1555 2.08 LINK MG MG A 402 O HOH A 671 1555 1555 2.07 CISPEP 1 PRO A 108 PRO A 109 0 13.21 CRYST1 51.086 57.799 60.691 90.00 109.89 90.00 P 1 21 1 2 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 0.019575 0.000000 0.007081 0.00000 SCALE2 0.000000 0.017301 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017522 0.00000 CONECT 58 2639 CONECT 250 2636 CONECT 896 2637 CONECT 900 2637 CONECT 919 2637 CONECT 1041 2667 CONECT 1206 2681 CONECT 1388 2695 CONECT 2192 2524 CONECT 2272 2653 CONECT 2524 2192 CONECT 2594 2598 2625 CONECT 2595 2601 2608 CONECT 2596 2611 2615 CONECT 2597 2618 2622 CONECT 2598 2594 2599 2632 CONECT 2599 2598 2600 2603 CONECT 2600 2599 2601 2602 CONECT 2601 2595 2600 2632 CONECT 2602 2600 CONECT 2603 2599 2604 CONECT 2604 2603 2605 CONECT 2605 2604 2606 2607 CONECT 2606 2605 2637 CONECT 2607 2605 CONECT 2608 2595 2609 2633 CONECT 2609 2608 2610 2612 CONECT 2610 2609 2611 2613 CONECT 2611 2596 2610 2633 CONECT 2612 2609 CONECT 2613 2610 2614 CONECT 2614 2613 CONECT 2615 2596 2616 2634 CONECT 2616 2615 2617 2619 CONECT 2617 2616 2618 2620 CONECT 2618 2597 2617 2634 CONECT 2619 2616 CONECT 2620 2617 2621 CONECT 2621 2620 CONECT 2622 2597 2623 2635 CONECT 2623 2622 2624 2626 CONECT 2624 2623 2625 2627 CONECT 2625 2594 2624 2635 CONECT 2626 2623 CONECT 2627 2624 2628 CONECT 2628 2627 2629 CONECT 2629 2628 2630 2631 CONECT 2630 2629 CONECT 2631 2629 CONECT 2632 2598 2601 2636 CONECT 2633 2608 2611 2636 CONECT 2634 2615 2618 2636 CONECT 2635 2622 2625 2636 CONECT 2636 250 2632 2633 2634 CONECT 2636 2635 CONECT 2637 896 900 919 2606 CONECT 2637 2934 2972 CONECT 2639 58 2640 2650 CONECT 2640 2639 2641 2647 CONECT 2641 2640 2642 2648 CONECT 2642 2641 2643 2649 CONECT 2643 2642 2644 2650 CONECT 2644 2643 2651 CONECT 2645 2646 2647 2652 CONECT 2646 2645 CONECT 2647 2640 2645 CONECT 2648 2641 CONECT 2649 2642 CONECT 2650 2639 2643 CONECT 2651 2644 CONECT 2652 2645 CONECT 2653 2272 2654 2664 CONECT 2654 2653 2655 2661 CONECT 2655 2654 2656 2662 CONECT 2656 2655 2657 2663 CONECT 2657 2656 2658 2664 CONECT 2658 2657 2665 CONECT 2659 2660 2661 2666 CONECT 2660 2659 CONECT 2661 2654 2659 CONECT 2662 2655 CONECT 2663 2656 CONECT 2664 2653 2657 CONECT 2665 2658 CONECT 2666 2659 CONECT 2667 1041 2668 2678 CONECT 2668 2667 2669 2675 CONECT 2669 2668 2670 2676 CONECT 2670 2669 2671 2677 CONECT 2671 2670 2672 2678 CONECT 2672 2671 2679 CONECT 2673 2674 2675 2680 CONECT 2674 2673 CONECT 2675 2668 2673 CONECT 2676 2669 CONECT 2677 2670 CONECT 2678 2667 2671 CONECT 2679 2672 CONECT 2680 2673 CONECT 2681 1206 2682 2692 CONECT 2682 2681 2683 2689 CONECT 2683 2682 2684 2690 CONECT 2684 2683 2685 2691 CONECT 2685 2684 2686 2692 CONECT 2686 2685 2693 CONECT 2687 2688 2689 2694 CONECT 2688 2687 CONECT 2689 2682 2687 CONECT 2690 2683 CONECT 2691 2684 CONECT 2692 2681 2685 CONECT 2693 2686 CONECT 2694 2687 CONECT 2695 1388 2696 2706 CONECT 2696 2695 2697 2703 CONECT 2697 2696 2698 2704 CONECT 2698 2697 2699 2705 CONECT 2699 2698 2700 2706 CONECT 2700 2699 2707 CONECT 2701 2702 2703 2708 CONECT 2702 2701 CONECT 2703 2696 2701 CONECT 2704 2697 CONECT 2705 2698 CONECT 2706 2695 2699 CONECT 2707 2700 CONECT 2708 2701 CONECT 2709 2710 2711 2712 2713 CONECT 2710 2709 CONECT 2711 2709 CONECT 2712 2709 CONECT 2713 2709 CONECT 2714 2715 2716 CONECT 2715 2714 CONECT 2716 2714 2717 2718 CONECT 2717 2716 CONECT 2718 2716 2719 CONECT 2719 2718 CONECT 2720 2721 2722 CONECT 2721 2720 CONECT 2722 2720 2723 2724 CONECT 2723 2722 CONECT 2724 2722 2725 CONECT 2725 2724 CONECT 2726 2727 2728 CONECT 2727 2726 CONECT 2728 2726 2729 2730 CONECT 2729 2728 CONECT 2730 2728 2731 CONECT 2731 2730 CONECT 2732 2733 CONECT 2733 2732 2734 2737 CONECT 2734 2733 2735 2740 CONECT 2735 2734 2736 CONECT 2736 2735 2742 CONECT 2737 2733 2738 CONECT 2738 2737 2739 CONECT 2739 2738 2740 CONECT 2740 2734 2739 2741 CONECT 2741 2740 2742 CONECT 2742 2736 2741 CONECT 2743 2744 CONECT 2744 2743 2745 2748 CONECT 2745 2744 2746 2751 CONECT 2746 2745 2747 CONECT 2747 2746 2753 CONECT 2748 2744 2749 CONECT 2749 2748 2750 CONECT 2750 2749 2751 CONECT 2751 2745 2750 2752 CONECT 2752 2751 2753 CONECT 2753 2747 2752 CONECT 2754 2755 CONECT 2755 2754 CONECT 2756 2757 CONECT 2757 2756 CONECT 2758 2759 CONECT 2759 2758 CONECT 2760 2761 CONECT 2761 2760 CONECT 2762 2763 CONECT 2763 2762 CONECT 2764 2765 CONECT 2765 2764 CONECT 2766 2768 CONECT 2767 2769 CONECT 2768 2766 CONECT 2769 2767 CONECT 2770 2771 CONECT 2771 2770 CONECT 2772 2773 CONECT 2773 2772 CONECT 2774 2775 CONECT 2775 2774 CONECT 2776 2777 CONECT 2777 2776 CONECT 2778 2779 CONECT 2779 2778 CONECT 2780 2781 CONECT 2781 2780 CONECT 2782 2783 CONECT 2783 2782 CONECT 2784 2785 CONECT 2785 2784 CONECT 2786 2787 CONECT 2787 2786 CONECT 2788 2789 CONECT 2789 2788 CONECT 2790 2791 CONECT 2791 2790 CONECT 2792 2793 CONECT 2793 2792 CONECT 2794 2795 CONECT 2795 2794 CONECT 2796 2797 CONECT 2797 2796 CONECT 2798 2799 CONECT 2799 2798 CONECT 2800 2801 CONECT 2801 2800 CONECT 2934 2637 CONECT 2972 2637 MASTER 352 0 37 13 5 0 0 6 3154 1 222 26 END