HEADER OXIDOREDUCTASE 12-SEP-17 5YD9 OBSLTE 04-JUL-18 5YD9 6A4Y TITLE CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE WITH IODIDE ION AT THE TITLE 2 SUBSTRATE BINDING SITE ON THE DISTAL HEME SIDE AT 1.91 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOPEROXIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 118-712; COMPND 5 SYNONYM: LPO; COMPND 6 EC: 1.11.1.7 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.K.SINGH,H.V.SIROHI,P.KAUR,S.SHARMA,T.P.SINGH REVDAT 2 04-JUL-18 5YD9 1 OBSLTE REVDAT 1 27-SEP-17 5YD9 0 JRNL AUTH P.K.SINGH,H.V.SIROHI,P.KAUR,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE WITH IODIDE ION JRNL TITL 2 AT THE SUBSTRATE BINDING SITE ON THE DISTAL HEME SIDE AT JRNL TITL 3 1.91 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 38471 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1899 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) : 1.92 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2882 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.3730 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.4010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4774 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 139 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.00000 REMARK 3 B22 (A**2) : -1.28000 REMARK 3 B33 (A**2) : 4.35000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.46000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.239 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.239 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.043 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5048 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4564 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6863 ; 1.765 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10612 ; 1.119 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 594 ; 7.174 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;36.508 ;23.724 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 824 ;17.725 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;17.175 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 725 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5559 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1057 ; 0.004 ; 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): 2386 ; 4.489 ; 5.729 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2378 ; 4.478 ; 5.731 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2972 ; 6.644 ; 8.581 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2973 ; 6.645 ; 8.584 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2662 ; 4.262 ; 6.059 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2656 ; 4.229 ; 6.064 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3885 ; 6.436 ; 8.982 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 21211 ;11.450 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 21116 ;11.442 ; 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 : 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 5YD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5-8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40370 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.910 REMARK 200 RESOLUTION RANGE LOW (A) : 65.170 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3BXI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM IODIDE, 20% PEG3350, PH REMARK 280 6.8, VAPOR DIFFUSION, HANGING DROP, 298K. 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 39.90000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 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 OD2 ASP A 108 CMD HEC A 601 1.83 REMARK 500 OE2 GLU A 258 CMB HEC A 601 1.88 REMARK 500 OD1 ASN A 29 O HOH A 701 2.05 REMARK 500 NH1 ARG A 204 OE2 GLU A 290 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CZ3 TRP A 368 O GLU A 594 2555 2.02 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 ASP A 16 N - CA - C ANGL. DEV. = -16.3 DEGREES REMARK 500 PRO A 168 C - N - CD ANGL. DEV. = -21.3 DEGREES REMARK 500 ARG A 348 NE - CZ - NH1 ANGL. DEV. = 3.5 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 PRO A 9 -4.89 -48.51 REMARK 500 VAL A 10 83.73 80.69 REMARK 500 ASN A 18 -93.48 -82.93 REMARK 500 SER A 19 159.88 66.94 REMARK 500 CYS A 28 0.07 80.21 REMARK 500 ALA A 56 -29.81 -149.81 REMARK 500 GLU A 118 -68.74 -97.94 REMARK 500 ASP A 137 -105.58 51.09 REMARK 500 ASN A 147 -2.72 94.79 REMARK 500 CYS A 167 -80.90 90.40 REMARK 500 TYR A 172 160.28 77.18 REMARK 500 GLN A 173 -131.18 -105.23 REMARK 500 LEU A 175 165.50 66.93 REMARK 500 ASP A 188 20.94 -144.58 REMARK 500 ASP A 221 79.45 -103.39 REMARK 500 ARG A 245 59.66 32.81 REMARK 500 GLU A 371 41.84 -105.50 REMARK 500 ASP A 389 31.51 -98.41 REMARK 500 LYS A 411 76.65 -152.03 REMARK 500 LYS A 485 -34.21 81.19 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 A 9 VAL A 10 149.05 REMARK 500 VAL A 10 PRO A 11 139.68 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 A 908 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 CA A 611 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 110 O REMARK 620 2 ASP A 110 OD1 72.8 REMARK 620 3 THR A 184 O 80.6 140.4 REMARK 620 4 THR A 184 OG1 131.1 147.2 71.9 REMARK 620 5 PHE A 186 O 120.9 79.7 89.8 99.0 REMARK 620 6 ASP A 188 OD1 136.8 71.3 142.3 76.7 74.9 REMARK 620 7 SER A 190 OG 76.3 81.4 120.3 83.8 148.6 75.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 601 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 351 NE2 REMARK 620 2 HEC A 601 NA 93.8 REMARK 620 3 HEC A 601 NB 94.5 89.1 REMARK 620 4 HEC A 601 NC 88.6 177.6 90.6 REMARK 620 5 HEC A 601 ND 87.4 90.4 178.1 89.8 REMARK 620 6 HOH A 774 O 176.4 86.3 89.1 91.3 89.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 614 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 615 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 616 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 617 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG A 602 bound REMARK 800 to ASN A 95 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Poly-Saccharide residues NAG A REMARK 800 603 through NAG A 604 bound to ASN A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG A 605 bound REMARK 800 to ASN A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Mono-Saccharide NAG A 606 bound REMARK 800 to ASN A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residues IOD A 610 and SCN A REMARK 800 618 DBREF 5YD9 A 1 595 UNP P80025 PERL_BOVIN 118 712 SEQRES 1 A 595 SER TRP GLU VAL GLY CYS GLY ALA PRO VAL PRO LEU VAL SEQRES 2 A 595 LYS CYS ASP GLU ASN SER PRO TYR ARG THR ILE THR GLY SEQRES 3 A 595 ASP CYS ASN ASN ARG ARG SER PRO ALA LEU GLY ALA ALA SEQRES 4 A 595 ASN ARG ALA LEU ALA ARG TRP LEU PRO ALA GLU TYR GLU SEQRES 5 A 595 ASP GLY LEU ALA LEU PRO PHE GLY TRP THR GLN ARG LYS SEQRES 6 A 595 THR ARG ASN GLY PHE ARG VAL PRO LEU ALA ARG GLU VAL SEQRES 7 A 595 SER ASN LYS ILE VAL GLY TYR LEU ASP GLU GLU GLY VAL SEQRES 8 A 595 LEU ASP GLN ASN ARG SER LEU LEU PHE MET GLN TRP GLY SEQRES 9 A 595 GLN ILE VAL ASP HIS ASP LEU ASP PHE ALA PRO GLU THR SEQRES 10 A 595 GLU LEU GLY SER ASN GLU HIS SER LYS THR GLN CYS GLU SEQRES 11 A 595 GLU TYR CYS ILE GLN GLY ASP ASN CYS PHE PRO ILE MET SEQRES 12 A 595 PHE PRO LYS ASN ASP PRO LYS LEU LYS THR GLN GLY LYS SEQRES 13 A 595 CYS MET PRO PHE PHE ARG ALA GLY PHE VAL CYS PRO THR SEQRES 14 A 595 PRO PRO TYR GLN SER LEU ALA ARG GLU GLN ILE ASN ALA SEQRES 15 A 595 VAL THR SER PHE LEU ASP ALA SER LEU VAL TYR GLY SER SEQRES 16 A 595 GLU PRO SEP LEU ALA SER ARG LEU ARG ASN LEU SER SER SEQRES 17 A 595 PRO LEU GLY LEU MET ALA VAL ASN GLN GLU ALA TRP ASP SEQRES 18 A 595 HIS GLY LEU ALA TYR LEU PRO PHE ASN ASN LYS LYS PRO SEQRES 19 A 595 SER PRO CYS GLU PHE ILE ASN THR THR ALA ARG VAL PRO SEQRES 20 A 595 CYS PHE LEU ALA GLY ASP PHE ARG ALA SER GLU GLN ILE SEQRES 21 A 595 LEU LEU ALA THR ALA HIS THR LEU LEU LEU ARG GLU HIS SEQRES 22 A 595 ASN ARG LEU ALA ARG GLU LEU LYS LYS LEU ASN PRO HIS SEQRES 23 A 595 TRP ASN GLY GLU LYS LEU TYR GLN GLU ALA ARG LYS ILE SEQRES 24 A 595 LEU GLY ALA PHE ILE GLN ILE ILE THR PHE ARG ASP TYR SEQRES 25 A 595 LEU PRO ILE VAL LEU GLY SER GLU MET GLN LYS TRP ILE SEQRES 26 A 595 PRO PRO TYR GLN GLY TYR ASN ASN SER VAL ASP PRO ARG SEQRES 27 A 595 ILE SER ASN VAL PHE THR PHE ALA PHE ARG PHE GLY HIS SEQRES 28 A 595 MET GLU VAL PRO SER THR VAL SER ARG LEU ASP GLU ASN SEQRES 29 A 595 TYR GLN PRO TRP GLY PRO GLU ALA GLU LEU PRO LEU HIS SEQRES 30 A 595 THR LEU PHE PHE ASN THR TRP ARG ILE ILE LYS ASP GLY SEQRES 31 A 595 GLY ILE ASP PRO LEU VAL ARG GLY LEU LEU ALA LYS LYS SEQRES 32 A 595 SER LYS LEU MET ASN GLN ASP LYS MET VAL THR SER GLU SEQRES 33 A 595 LEU ARG ASN LYS LEU PHE GLN PRO THR HIS LYS ILE HIS SEQRES 34 A 595 GLY PHE ASP LEU ALA ALA ILE ASN LEU GLN ARG CYS ARG SEQRES 35 A 595 ASP HIS GLY MET PRO GLY TYR ASN SER TRP ARG GLY PHE SEQRES 36 A 595 CYS GLY LEU SER GLN PRO LYS THR LEU LYS GLY LEU GLN SEQRES 37 A 595 THR VAL LEU LYS ASN LYS ILE LEU ALA LYS LYS LEU MET SEQRES 38 A 595 ASP LEU TYR LYS THR PRO ASP ASN ILE ASP ILE TRP ILE SEQRES 39 A 595 GLY GLY ASN ALA GLU PRO MET VAL GLU ARG GLY ARG VAL SEQRES 40 A 595 GLY PRO LEU LEU ALA CYS LEU LEU GLY ARG GLN PHE GLN SEQRES 41 A 595 GLN ILE ARG ASP GLY ASP ARG PHE TRP TRP GLU ASN PRO SEQRES 42 A 595 GLY VAL PHE THR GLU LYS GLN ARG ASP SER LEU GLN LYS SEQRES 43 A 595 VAL SER PHE SER ARG LEU ILE CYS ASP ASN THR HIS ILE SEQRES 44 A 595 THR LYS VAL PRO LEU HIS ALA PHE GLN ALA ASN ASN TYR SEQRES 45 A 595 PRO HIS ASP PHE VAL ASP CYS SER THR VAL ASP LYS LEU SEQRES 46 A 595 ASP LEU SER PRO TRP ALA SER ARG GLU ASN MODRES 5YD9 SEP A 198 SER MODIFIED RESIDUE HET SEP A 198 10 HET HEC A 601 43 HET NAG A 602 14 HET NAG A 603 14 HET NAG A 604 14 HET NAG A 605 14 HET NAG A 606 14 HET IOD A 607 1 HET IOD A 608 1 HET IOD A 609 1 HET IOD A 610 1 HET CA A 611 1 HET SCN A 612 3 HET SCN A 613 3 HET SCN A 614 3 HET SCN A 615 3 HET SCN A 616 3 HET SCN A 617 3 HET SCN A 618 3 HETNAM SEP PHOSPHOSERINE HETNAM HEC HEME C HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM IOD IODIDE ION HETNAM CA CALCIUM ION HETNAM SCN THIOCYANATE ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 NAG 5(C8 H15 N O6) FORMUL 7 IOD 4(I 1-) FORMUL 11 CA CA 2+ FORMUL 12 SCN 7(C N S 1-) FORMUL 19 HOH *208(H2 O) HELIX 1 AA1 LEU A 74 VAL A 83 1 10 HELIX 2 AA2 LEU A 98 ASP A 112 1 15 HELIX 3 AA3 HIS A 124 CYS A 133 1 10 HELIX 4 AA4 ASP A 148 GLN A 154 1 7 HELIX 5 AA5 ALA A 189 GLY A 194 1 6 HELIX 6 AA6 GLU A 196 ARG A 204 1 9 HELIX 7 AA7 SER A 235 ILE A 240 1 6 HELIX 8 AA8 GLN A 259 ASN A 284 1 26 HELIX 9 AA9 ASN A 288 ASP A 311 1 24 HELIX 10 AB1 TYR A 312 GLY A 318 1 7 HELIX 11 AB2 GLU A 320 ILE A 325 1 6 HELIX 12 AB3 VAL A 342 PHE A 347 1 6 HELIX 13 AB4 ARG A 348 VAL A 354 5 7 HELIX 14 AB5 HIS A 377 PHE A 380 5 4 HELIX 15 AB6 THR A 383 LYS A 388 1 6 HELIX 16 AB7 ILE A 392 LYS A 402 1 11 HELIX 17 AB8 THR A 414 ASN A 419 1 6 HELIX 18 AB9 ASP A 432 HIS A 444 1 13 HELIX 19 AC1 GLY A 448 CYS A 456 1 9 HELIX 20 AC2 THR A 463 LYS A 472 1 10 HELIX 21 AC3 ASN A 473 LYS A 485 1 13 HELIX 22 AC4 THR A 486 ILE A 490 5 5 HELIX 23 AC5 ASP A 491 GLU A 499 1 9 HELIX 24 AC6 GLY A 508 GLY A 525 1 18 HELIX 25 AC7 THR A 537 GLN A 545 1 9 HELIX 26 AC8 SER A 548 THR A 557 1 10 HELIX 27 AC9 SER A 580 VAL A 582 5 3 HELIX 28 AD1 LEU A 587 ALA A 591 5 5 SHEET 1 AA1 2 ARG A 41 ALA A 42 0 SHEET 2 AA1 2 ILE A 180 ASN A 181 -1 O ASN A 181 N ARG A 41 SHEET 1 AA2 2 LEU A 92 SER A 97 0 SHEET 2 AA2 2 LYS A 403 LYS A 405 -1 O SER A 404 N ASP A 93 SHEET 1 AA3 2 ILE A 142 MET A 143 0 SHEET 2 AA3 2 CYS A 157 MET A 158 -1 O MET A 158 N ILE A 142 SHEET 1 AA4 2 THR A 357 SER A 359 0 SHEET 2 AA4 2 GLU A 373 PRO A 375 -1 O LEU A 374 N VAL A 358 SHEET 1 AA5 2 LEU A 421 PHE A 422 0 SHEET 2 AA5 2 HIS A 429 PHE A 431 -1 O PHE A 431 N LEU A 421 SHEET 1 AA6 2 LYS A 561 PRO A 563 0 SHEET 2 AA6 2 PHE A 576 ASP A 578 -1 O VAL A 577 N VAL A 562 SSBOND 1 CYS A 6 CYS A 167 1555 1555 2.04 SSBOND 2 CYS A 15 CYS A 28 1555 1555 2.03 SSBOND 3 CYS A 129 CYS A 139 1555 1555 2.00 SSBOND 4 CYS A 133 CYS A 157 1555 1555 2.02 SSBOND 5 CYS A 237 CYS A 248 1555 1555 2.02 SSBOND 6 CYS A 456 CYS A 513 1555 1555 2.05 SSBOND 7 CYS A 554 CYS A 579 1555 1555 2.03 LINK ND2 ASN A 95 C1 NAG A 602 1555 1555 1.45 LINK O ASP A 110 CA CA A 611 1555 1555 2.46 LINK OD1 ASP A 110 CA CA A 611 1555 1555 2.41 LINK O THR A 184 CA CA A 611 1555 1555 2.34 LINK OG1 THR A 184 CA CA A 611 1555 1555 2.42 LINK O PHE A 186 CA CA A 611 1555 1555 2.16 LINK OD1 ASP A 188 CA CA A 611 1555 1555 2.66 LINK OG SER A 190 CA CA A 611 1555 1555 2.32 LINK C PRO A 197 N SEP A 198 1555 1555 1.32 LINK C SEP A 198 N LEU A 199 1555 1555 1.33 LINK ND2 ASN A 205 C1 NAG A 603 1555 1555 1.43 LINK ND2 ASN A 241 C1 NAG A 605 1555 1555 1.44 LINK ND2 ASN A 332 C1 NAG A 606 1555 1555 1.48 LINK NE2 HIS A 351 FE HEC A 601 1555 1555 2.32 LINK FE HEC A 601 O HOH A 774 1555 1555 2.43 LINK O4 NAG A 603 C1 NAG A 604 1555 1555 1.43 LINK I IOD A 610 N SCN A 618 1555 1555 2.04 CISPEP 1 LYS A 233 PRO A 234 0 -12.54 CISPEP 2 TYR A 572 PRO A 573 0 1.90 SITE 1 AC1 19 MET A 101 GLY A 104 GLN A 105 ASP A 108 SITE 2 AC1 19 ASP A 112 PHE A 113 ALA A 114 ARG A 255 SITE 3 AC1 19 GLU A 258 THR A 344 PHE A 347 ARG A 348 SITE 4 AC1 19 GLY A 350 HIS A 351 LEU A 417 ILE A 436 SITE 5 AC1 19 ARG A 440 HOH A 705 HOH A 774 SITE 1 AC2 1 ARG A 255 SITE 1 AC3 1 ASN A 80 SITE 1 AC4 2 TRP A 530 SCN A 616 SITE 1 AC5 5 ASP A 110 THR A 184 PHE A 186 ASP A 188 SITE 2 AC5 5 SER A 190 SITE 1 AC6 3 PHE A 254 SER A 257 HOH A 821 SITE 1 AC7 2 HIS A 377 THR A 378 SITE 1 AC8 4 ARG A 76 ASN A 419 HOH A 702 HOH A 732 SITE 1 AC9 3 SER A 359 GLU A 373 LYS A 402 SITE 1 AD1 5 GLN A 305 ILE A 306 PHE A 309 TRP A 530 SITE 2 AD1 5 IOD A 609 SITE 1 AD2 7 ARG A 45 TRP A 46 LEU A 47 VAL A 342 SITE 2 AD2 7 MET A 446 PRO A 447 TRP A 452 SITE 1 AD3 3 ASN A 95 ILE A 315 GLN A 568 SITE 1 AD4 6 ASN A 205 SER A 208 ALA A 214 VAL A 215 SITE 2 AD4 6 HOH A 706 HOH A 818 SITE 1 AD5 5 ASN A 241 ALA A 244 TRP A 384 LYS A 388 SITE 2 AD5 5 HOH A 752 SITE 1 AD6 2 ASN A 332 HOH A 817 SITE 1 AD7 4 PRO A 236 PHE A 239 PRO A 424 HIS A 426 CRYST1 53.740 79.800 65.180 90.00 91.43 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 0.018608 0.000000 0.000465 0.00000 SCALE2 0.000000 0.012531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015347 0.00000