10 20 30 40 50 60 70 80 3M5Q - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 12-MAR-10 3M5Q
TITLE 0.93 A STRUCTURE OF MANGANESE-BOUND MANGANESE PEROXIDASE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANGANESE PEROXIDASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MNP-1, MNP1, MANGANESE PEROXIDASE ISOZYME 1, PEROXIDASE COMPND 5 MANGANESE-DEPENDENT 1, PEROXIDASE MANGANESE-DEPENDENT I; COMPND 6 EC: 1.11.1.13
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHANEROCHAETE CHRYSOSPORIUM; SOURCE 3 ORGANISM_COMMON: WHITE-ROT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5306
KEYWDS PEROXIDASE, HEME, MN(II)-BINDING SITE, CA(II)-BINDING SITE, KEYWDS 2 GLYCOSYLATION, ULTRAHIGH RESOLUTION, CALCIUM, DISULFIDE BOND, KEYWDS 3 GLYCOPROTEIN, HYDROGEN PEROXIDE, IRON, LIGNIN DEGRADATION, KEYWDS 4 MANGANESE, METAL-BINDING, OXIDOREDUCTASE, SECRETED
EXPDTA X-RAY DIFFRACTION
AUTHOR M.SUNDARAMOORTHY,M.H.GOLD,T.L.POULOS
REVDAT 2 26-MAY-10 3M5Q 1 JRNL REVDAT 1 14-APR-10 3M5Q 0
JRNL AUTH M.SUNDARAMOORTHY,M.H.GOLD,T.L.POULOS JRNL TITL ULTRAHIGH (0.93A) RESOLUTION STRUCTURE OF MANGANESE JRNL TITL 2 PEROXIDASE FROM PHANEROCHAETE CHRYSOSPORIUM: IMPLICATIONS JRNL TITL 3 FOR THE CATALYTIC MECHANISM. JRNL REF J.INORG.BIOCHEM. V. 104 683 2010 JRNL REFN ISSN 0162-0134 JRNL PMID 20356630 JRNL DOI 10.1016/J.JINORGBIO.2010.02.011
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SUNDARAMOORTHY,H.L.YOUNGS,M.H.GOLD,T.L.POULOS REMARK 1 TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE: REMARK 1 TITL 2 SUBSTRATE AND INHIBITOR COMPLEXES. REMARK 1 REF BIOCHEMISTRY V. 44 6463 2005 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 15850380 REMARK 1 DOI 10.1021/BI047318E REMARK 1 REFERENCE 2 REMARK 1 AUTH M.SUNDARAMOORTHY,K.KISHI,M.H.GOLD,T.L.POULOS REMARK 1 TITL THE CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE FROM REMARK 1 TITL 2 PHANEROCHAETE CHRYSOSPORIUM AT 2.06-A RESOLUTION. REMARK 1 REF J.BIOL.CHEM. V. 269 32759 1994 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 7806497
REMARK 2 REMARK 2 RESOLUTION. 0.93 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.124 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3967 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 243170 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.107 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 0.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 191300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2629 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 91 REMARK 3 SOLVENT ATOMS : 476 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 29226 REMARK 3 NUMBER OF RESTRAINTS : 35571 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.096 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.106 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.062 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.050 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.112 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 3.6%
REMARK 4 REMARK 4 3M5Q COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB058141.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 264958 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.930 REMARK 200 RESOLUTION RANGE LOW (A) : 160.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.51200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: SHELX-97 REMARK 200 STARTING MODEL: 1YYD REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.2 M AMMONIUM SULFATE, REMARK 280 0.1 M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 80.28500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 80.28500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.65000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 39 CD GLU A 39 OE1 0.122 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 CYS A 3 CB - CA - C ANGL. DEV. = 8.7 DEGREES REMARK 500 GLY A 6 C - N - CA ANGL. DEV. = 22.8 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLU A 39 OE1 - CD - OE2 ANGL. DEV. = -13.0 DEGREES REMARK 500 ARG A 53 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 270 CD - NE - CZ ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 283 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 323 CB - CG - CD ANGL. DEV. = 32.9 DEGREES REMARK 500 ARG A 323 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 SER A 345 O - C - N ANGL. DEV. = 10.6 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 CYS A 33 54.11 -90.16 REMARK 500 VAL A 73 -89.54 -96.32 REMARK 500 SER A 309 -2.03 90.85 REMARK 500 SER A 318 10.28 -140.82 REMARK 500 CYS A 348 63.50 -166.66 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 A1156 DISTANCE = 5.65 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 396 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 173 NE2 REMARK 620 2 HEM A 396 NA 98.6 REMARK 620 3 HEM A 396 NB 93.8 89.7 REMARK 620 4 HEM A 396 NC 97.2 164.2 89.9 REMARK 620 5 HEM A 396 ND 99.1 88.1 167.1 88.7 REMARK 620 6 HOH A1137 O 174.4 77.1 82.7 87.1 84.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 381 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HEM A 396 O1D REMARK 620 2 GLU A 39 OE2 85.4 REMARK 620 3 HOH A1040 O 100.3 173.8 REMARK 620 4 HOH A1108 O 85.5 93.7 89.1 REMARK 620 5 ASP A 179 OD2 168.4 90.7 84.2 83.8 REMARK 620 6 GLU A 35 OE1 95.6 89.9 87.3 176.3 95.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 372 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 47 OD2 REMARK 620 2 HOH A1127 O 174.9 REMARK 620 3 HOH A1085 O 91.9 86.3 REMARK 620 4 ASP A 64 OD1 83.9 95.4 150.8 REMARK 620 5 ASP A 47 O 82.0 102.0 74.3 133.0 REMARK 620 6 GLY A 62 O 95.8 88.6 139.1 70.0 67.2 REMARK 620 7 SER A 66 OG 90.0 85.0 75.0 76.1 147.9 144.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 371 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 174 O REMARK 620 2 THR A 193 O 80.9 REMARK 620 3 ASP A 191 OD2 92.9 127.4 REMARK 620 4 ASP A 198 OD1 142.9 126.4 88.2 REMARK 620 5 SER A 174 OG 73.3 144.8 78.3 70.7 REMARK 620 6 THR A 193 OG1 145.6 69.4 91.7 71.2 140.8 REMARK 620 7 THR A 196 O 84.3 76.6 155.2 79.6 77.3 104.5 REMARK 620 8 ASP A 191 OD1 78.6 76.3 51.4 127.9 120.0 77.9 149.9 REMARK 620 N 1 2 3 4 5 6 7
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 372 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 396
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1MNP RELATED DB: PDB REMARK 900 RELATED ID: 1YYD RELATED DB: PDB REMARK 900 RELATED ID: 1YYG RELATED DB: PDB REMARK 900 RELATED ID: 1YZP RELATED DB: PDB REMARK 900 RELATED ID: 1YZR RELATED DB: PDB REMARK 900 RELATED ID: 3M8M RELATED DB: PDB
DBREF 3M5Q A 1 357 UNP Q02567 PEM1_PHACH 22 378
SEQRES 1 A 357 ALA VAL CYS PRO ASP GLY THR ARG VAL SER HIS ALA ALA SEQRES 2 A 357 CYS CYS ALA PHE ILE PRO LEU ALA GLN ASP LEU GLN GLU SEQRES 3 A 357 THR ILE PHE GLN ASN GLU CYS GLY GLU ASP ALA HIS GLU SEQRES 4 A 357 VAL ILE ARG LEU THR PHE HIS ASP ALA ILE ALA ILE SER SEQRES 5 A 357 ARG SER GLN GLY PRO LYS ALA GLY GLY GLY ALA ASP GLY SEQRES 6 A 357 SER MET LEU LEU PHE PRO THR VAL GLU PRO ASN PHE SER SEQRES 7 A 357 ALA ASN ASN GLY ILE ASP ASP SER VAL ASN ASN LEU ILE SEQRES 8 A 357 PRO PHE MET GLN LYS HIS ASN THR ILE SER ALA ALA ASP SEQRES 9 A 357 LEU VAL GLN PHE ALA GLY ALA VAL ALA LEU SER ASN CYS SEQRES 10 A 357 PRO GLY ALA PRO ARG LEU GLU PHE LEU ALA GLY ARG PRO SEQRES 11 A 357 ASN LYS THR ILE ALA ALA VAL ASP GLY LEU ILE PRO GLU SEQRES 12 A 357 PRO GLN ASP SER VAL THR LYS ILE LEU GLN ARG PHE GLU SEQRES 13 A 357 ASP ALA GLY GLY PHE THR PRO PHE GLU VAL VAL SER LEU SEQRES 14 A 357 LEU ALA SER HIS SER VAL ALA ARG ALA ASP LYS VAL ASP SEQRES 15 A 357 GLN THR ILE ASP ALA ALA PRO PHE ASP SER THR PRO PHE SEQRES 16 A 357 THR PHE ASP THR GLN VAL PHE LEU GLU VAL LEU LEU LYS SEQRES 17 A 357 GLY VAL GLY PHE PRO GLY SER ALA ASN ASN THR GLY GLU SEQRES 18 A 357 VAL ALA SER PRO LEU PRO LEU GLY SER GLY SER ASP THR SEQRES 19 A 357 GLY GLU MET ARG LEU GLN SER ASP PHE ALA LEU ALA HIS SEQRES 20 A 357 ASP PRO ARG THR ALA CYS ILE TRP GLN GLY PHE VAL ASN SEQRES 21 A 357 GLU GLN ALA PHE MET ALA ALA SER PHE ARG ALA ALA MET SEQRES 22 A 357 SER LYS LEU ALA VAL LEU GLY HIS ASN ARG ASN SER LEU SEQRES 23 A 357 ILE ASP CYS SER ASP VAL VAL PRO VAL PRO LYS PRO ALA SEQRES 24 A 357 THR GLY GLN PRO ALA MET PHE PRO ALA SER THR GLY PRO SEQRES 25 A 357 GLN ASP LEU GLU LEU SER CYS PRO SER GLU ARG PHE PRO SEQRES 26 A 357 THR LEU THR THR GLN PRO GLY ALA SER GLN SER LEU ILE SEQRES 27 A 357 ALA HIS CYS PRO ASP GLY SER MET SER CYS PRO GLY VAL SEQRES 28 A 357 GLN PHE ASN GLY PRO ALA
MODRES 3M5Q ASN A 131 ASN GLYCOSYLATION SITE MODRES 3M5Q SER A 336 SER GLYCOSYLATION SITE
HET NAG A 361 14 HET NAG A 362 14 HET MAN A 364 12 HET CA A 371 1 HET CA A 372 1 HET MN A 381 1 HET GOL A 391 6 HET HEM A 396 44
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM MAN ALPHA-D-MANNOSE HETNAM CA CALCIUM ION HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE
HETSYN HEM HEME
FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 MAN C6 H12 O6 FORMUL 4 CA 2(CA 2+) FORMUL 6 MN MN 2+ FORMUL 7 GOL C3 H8 O3 FORMUL 8 HEM C34 H32 FE N4 O4 FORMUL 9 HOH *476(H2 O)
HELIX 1 1 HIS A 11 CYS A 15 5 5 HELIX 2 2 ALA A 16 ILE A 28 1 13 HELIX 3 3 GLY A 34 ALA A 50 1 17 HELIX 4 4 GLY A 56 GLY A 60 5 5 HELIX 5 5 GLY A 65 PHE A 70 1 6 HELIX 6 6 VAL A 73 ASN A 81 5 9 HELIX 7 7 ILE A 83 HIS A 97 1 15 HELIX 8 8 SER A 101 ASN A 116 1 16 HELIX 9 9 SER A 147 GLY A 160 1 14 HELIX 10 10 THR A 162 LEU A 170 1 9 HELIX 11 11 ALA A 171 VAL A 175 5 5 HELIX 12 12 THR A 199 LEU A 206 1 8 HELIX 13 13 GLN A 240 ASP A 248 1 9 HELIX 14 14 THR A 251 PHE A 258 1 8 HELIX 15 15 GLU A 261 ALA A 277 1 17 HELIX 16 16 ASN A 282 LEU A 286 5 5 HELIX 17 17 SER A 290 VAL A 293 5 4 HELIX 18 18 GLY A 311 LEU A 315 5 5
SHEET 1 A 2 LEU A 126 ALA A 127 0 SHEET 2 A 2 ILE A 287 ASP A 288 -1 O ILE A 287 N ALA A 127 SHEET 1 B 2 ARG A 177 ALA A 178 0 SHEET 2 B 2 ALA A 188 PRO A 189 -1 O ALA A 188 N ALA A 178 SHEET 1 C 2 GLU A 221 VAL A 222 0 SHEET 2 C 2 ARG A 238 LEU A 239 -1 O ARG A 238 N VAL A 222
SSBOND 1 CYS A 3 CYS A 15 1555 1555 2.16 SSBOND 2 CYS A 14 CYS A 289 1555 1555 2.06 SSBOND 3 CYS A 33 CYS A 117 1555 1555 2.08 SSBOND 4 CYS A 253 CYS A 319 1555 1555 2.12 SSBOND 5 CYS A 341 CYS A 348 1555 1555 2.05
LINK O4 NAG A 361 C1 NAG A 362 1555 1555 1.40 LINK ND2 ASN A 131 C1 NAG A 361 1555 1555 1.45 LINK NE2 HIS A 173 FE HEM A 396 1555 1555 2.08 LINK MN MN A 381 O1D HEM A 396 1555 1555 2.13 LINK OE2 GLU A 39 MN MN A 381 1555 1555 2.14 LINK MN MN A 381 O HOH A1040 1555 1555 2.26 LINK MN MN A 381 O HOH A1108 1555 1555 2.26 LINK OD2 ASP A 179 MN MN A 381 1555 1555 2.27 LINK OE1 GLU A 35 MN MN A 381 1555 1555 2.27 LINK OD2 ASP A 47 CA CA A 372 1555 1555 2.31 LINK CA CA A 372 O HOH A1127 1555 1555 2.33 LINK O SER A 174 CA CA A 371 1555 1555 2.37 LINK O THR A 193 CA CA A 371 1555 1555 2.38 LINK CA CA A 372 O HOH A1085 1555 1555 2.41 LINK OD1 ASP A 64 CA CA A 372 1555 1555 2.42 LINK OD2 ASP A 191 CA CA A 371 1555 1555 2.44 LINK O ASP A 47 CA CA A 372 1555 1555 2.44 LINK OD1 ASP A 198 CA CA A 371 1555 1555 2.46 LINK O GLY A 62 CA CA A 372 1555 1555 2.46 LINK OG SER A 174 CA CA A 371 1555 1555 2.47 LINK OG SER A 66 CA CA A 372 1555 1555 2.49 LINK OG1 THR A 193 CA CA A 371 1555 1555 2.49 LINK O THR A 196 CA CA A 371 1555 1555 2.51 LINK FE HEM A 396 O HOH A1137 1555 1555 2.57 LINK OD1 ASP A 191 CA CA A 371 1555 1555 2.67 LINK OG SER A 336 C1 MAN A 364 1555 1555 1.39
SITE 1 AC1 8 ASN A 98 THR A 99 ASN A 131 NAG A 362 SITE 2 AC1 8 HOH A1090 HOH A1117 HOH A1240 HOH A1297 SITE 1 AC2 9 MET A 94 GLN A 95 ASN A 98 NAG A 361 SITE 2 AC2 9 HOH A1226 HOH A1409 HOH A1557 HOH A1558 SITE 3 AC2 9 HOH A1566 SITE 1 AC3 7 HIS A 11 PRO A 331 GLY A 332 SER A 334 SITE 2 AC3 7 GLN A 335 SER A 336 HOH A1238 SITE 1 AC4 5 SER A 174 ASP A 191 THR A 193 THR A 196 SITE 2 AC4 5 ASP A 198 SITE 1 AC5 6 ASP A 47 GLY A 62 ASP A 64 SER A 66 SITE 2 AC5 6 HOH A1085 HOH A1127 SITE 1 AC6 6 GLU A 35 GLU A 39 ASP A 179 HEM A 396 SITE 2 AC6 6 HOH A1040 HOH A1108 SITE 1 AC7 6 ASP A 23 THR A 27 PRO A 92 LYS A 96 SITE 2 AC7 6 GLU A 156 HOH A1092 SITE 1 AC8 25 GLU A 35 HIS A 38 GLU A 39 ARG A 42 SITE 2 AC8 25 PHE A 45 GLU A 143 PRO A 144 PHE A 155 SITE 3 AC8 25 LEU A 169 LEU A 170 SER A 172 HIS A 173 SITE 4 AC8 25 ALA A 176 ARG A 177 ALA A 178 ASP A 179 SITE 5 AC8 25 LYS A 180 VAL A 181 SER A 241 MN A 381 SITE 6 AC8 25 HOH A1074 HOH A1108 HOH A1137 HOH A1190 SITE 7 AC8 25 HOH A1223
CRYST1 160.570 45.300 52.830 90.00 97.31 90.00 C 1 2 1 4
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 0.006228 0.000000 0.000799 0.00000
SCALE2 0.000000 0.022075 0.000000 0.00000
SCALE3 0.000000 0.000000 0.019084 0.00000