HEADER OXIDOREDUCTASE 07-JUL-14 4USC TITLE CRYSTAL STRUCTURE OF PEROXIDASE FROM PALM TREE CHAMAEROPS EXCELSA CAVEAT 4USC NAG C 2 HAS WRONG CHIRALITY AT ATOM C1 MAN C 3 HAS WRONG CAVEAT 2 4USC CHIRALITY AT ATOM C1 NAG A 1314 HAS WRONG CHIRALITY AT ATOM CAVEAT 3 4USC C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXIDASE; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRACHYCARPUS FORTUNEI; SOURCE 3 ORGANISM_COMMON: WINDMILL PALM; SOURCE 4 ORGANISM_TAXID: 14027; SOURCE 5 ORGAN: LEAF KEYWDS OXIDOREDUCTASE, PLANT PEROXIDASE, GLYCOSYLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.BERNARDES,J.C.SANTOS,L.C.TEXTOR,N.H.CUADRADO,E.Y.KOSTETSKY, AUTHOR 2 M.G.ROIG,J.R.C.MUNIZ,V.L.SHNYROV,I.POLIKARPOV REVDAT 4 09-OCT-24 4USC 1 REMARK REVDAT 3 10-JAN-24 4USC 1 HETSYN REVDAT 2 29-JUL-20 4USC 1 CAVEAT COMPND REMARK HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 27-MAY-15 4USC 0 JRNL AUTH A.BERNARDES,L.C.TEXTOR,J.C.SANTOS,N.H.CUADRADO, JRNL AUTH 2 E.Y.KOSTETSKY,M.G.ROIG,V.N.BAVRO,J.R.C.MUNIZ,V.L.SHNYROV, JRNL AUTH 3 I.POLIKARPOV JRNL TITL CRYSTAL STRUCTURE ANALYSIS OF PEROXIDASE FROM THE PALM TREE JRNL TITL 2 CHAMAEROPS EXCELSA. JRNL REF BIOCHIMIE V. 111 58 2015 JRNL REFN ISSN 0300-9084 JRNL PMID 25660651 JRNL DOI 10.1016/J.BIOCHI.2015.01.014 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 25246 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1369 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1857 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4461 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 314 REMARK 3 SOLVENT ATOMS : 85 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.23000 REMARK 3 B22 (A**2) : 10.61000 REMARK 3 B33 (A**2) : -6.38000 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): 0.547 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.295 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.258 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.103 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4875 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4469 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6694 ; 1.731 ; 2.024 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10179 ; 2.633 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 604 ; 5.849 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;40.535 ;25.080 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 685 ;14.934 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.198 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 827 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5527 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1069 ; 0.023 ; 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): 2422 ; 2.210 ; 4.288 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2421 ; 2.211 ; 4.287 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3024 ; 3.506 ; 6.429 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2453 ; 2.948 ; 4.776 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 187 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5954 -5.5463 35.5749 REMARK 3 T TENSOR REMARK 3 T11: 0.1236 T22: 0.0765 REMARK 3 T33: 0.1018 T12: 0.0400 REMARK 3 T13: -0.0034 T23: 0.0254 REMARK 3 L TENSOR REMARK 3 L11: 1.0549 L22: 0.0268 REMARK 3 L33: 1.1470 L12: 0.1515 REMARK 3 L13: -0.2573 L23: -0.0098 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.1459 S13: -0.0426 REMARK 3 S21: -0.0111 S22: -0.0079 S23: -0.0090 REMARK 3 S31: 0.0668 S32: 0.0312 S33: 0.0059 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 188 A 303 REMARK 3 ORIGIN FOR THE GROUP (A): 4.2632 -7.7024 22.8680 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.0343 REMARK 3 T33: 0.0791 T12: 0.0398 REMARK 3 T13: 0.0208 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 0.8657 L22: 0.0564 REMARK 3 L33: 2.0656 L12: 0.0776 REMARK 3 L13: 0.0887 L23: 0.0325 REMARK 3 S TENSOR REMARK 3 S11: -0.0304 S12: -0.0217 S13: -0.0437 REMARK 3 S21: -0.0578 S22: 0.0171 S23: -0.0071 REMARK 3 S31: 0.1855 S32: 0.1310 S33: 0.0133 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 113 REMARK 3 ORIGIN FOR THE GROUP (A): 4.6727 -4.8349 -23.9575 REMARK 3 T TENSOR REMARK 3 T11: 0.1407 T22: 0.1051 REMARK 3 T33: 0.0739 T12: -0.0167 REMARK 3 T13: -0.0157 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 0.8894 L22: 0.5207 REMARK 3 L33: 0.9231 L12: -0.1777 REMARK 3 L13: -0.8778 L23: 0.2582 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: 0.1431 S13: 0.0186 REMARK 3 S21: -0.0240 S22: 0.0720 S23: -0.0665 REMARK 3 S31: 0.0820 S32: -0.1120 S33: -0.0558 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 114 B 160 REMARK 3 ORIGIN FOR THE GROUP (A): -8.2802 -10.1118 -19.0421 REMARK 3 T TENSOR REMARK 3 T11: 0.0747 T22: 0.1641 REMARK 3 T33: 0.0448 T12: -0.0817 REMARK 3 T13: -0.0058 T23: -0.0397 REMARK 3 L TENSOR REMARK 3 L11: 1.4506 L22: 0.7602 REMARK 3 L33: 3.2147 L12: -0.5447 REMARK 3 L13: -0.7196 L23: -0.7681 REMARK 3 S TENSOR REMARK 3 S11: -0.0752 S12: 0.3264 S13: -0.2321 REMARK 3 S21: -0.0170 S22: 0.0459 S23: 0.0920 REMARK 3 S31: 0.2403 S32: -0.5296 S33: 0.0294 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 161 B 303 REMARK 3 ORIGIN FOR THE GROUP (A): -4.9036 -6.9524 -6.2091 REMARK 3 T TENSOR REMARK 3 T11: 0.1553 T22: 0.0350 REMARK 3 T33: 0.0833 T12: -0.0279 REMARK 3 T13: 0.0231 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.0131 L22: 0.0063 REMARK 3 L33: 1.9979 L12: -0.0639 REMARK 3 L13: 0.1183 L23: 0.0312 REMARK 3 S TENSOR REMARK 3 S11: -0.0278 S12: 0.0216 S13: -0.0354 REMARK 3 S21: 0.0121 S22: 0.0006 S23: -0.0057 REMARK 3 S31: 0.1436 S32: -0.2569 S33: 0.0272 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U REMARK 3 VALUES WITH TLS ADDED REMARK 4 REMARK 4 4USC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1290061183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.4586 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29525 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 80.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.01000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3HDL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMMONIUM SULFATE, 0.085 M TRIS REMARK 280 PH 8.0, 17% PEG MME 2K, 15% GLYCEROL 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 35.09000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.15500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.32500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.15500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.09000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.32500 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: 8970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 1 CG OD1 OD2 REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 LYS A 262 CE NZ REMARK 470 GLN A 277 CG CD OE1 NE2 REMARK 470 ASP B 59 CG OD1 OD2 REMARK 470 LYS B 262 CG CD CE NZ REMARK 470 GLN B 277 OE1 NE2 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 185 C1 NAG A 1315 1.99 REMARK 500 ND2 ASN A 127 O5 NAG A 1314 2.08 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 11 73.90 -154.55 REMARK 500 ASN A 211 0.71 -63.89 REMARK 500 CYS B 11 73.20 -151.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG A 1315 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 A1305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 43 OD1 REMARK 620 2 ASP A 43 O 75.1 REMARK 620 3 VAL A 46 O 153.6 78.8 REMARK 620 4 GLY A 48 O 80.0 69.7 87.0 REMARK 620 5 ASP A 50 OD1 85.5 139.6 112.4 72.2 REMARK 620 6 SER A 52 OG 109.4 138.9 93.2 150.8 80.8 REMARK 620 7 HOH A2009 O 93.2 68.8 81.3 138.3 148.8 70.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A1318 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 169 NE2 REMARK 620 2 HEM A1318 NA 92.6 REMARK 620 3 HEM A1318 NB 88.6 89.0 REMARK 620 4 HEM A1318 NC 86.6 178.7 89.9 REMARK 620 5 HEM A1318 ND 92.0 91.4 179.3 89.7 REMARK 620 6 PEO A1320 O1 156.3 69.8 75.8 110.7 103.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 170 OG REMARK 620 2 SER A 170 O 78.7 REMARK 620 3 ASP A 223 OD2 91.5 91.4 REMARK 620 4 THR A 226 OG1 135.7 145.1 83.7 REMARK 620 5 THR A 226 O 160.3 82.0 84.8 63.2 REMARK 620 6 VAL A 229 O 96.7 84.0 169.6 94.7 85.3 REMARK 620 7 ASP A 231 OD1 64.7 140.1 104.3 74.0 134.9 85.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1309 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 43 O REMARK 620 2 ASP B 43 OD1 74.4 REMARK 620 3 VAL B 46 O 77.4 151.2 REMARK 620 4 GLY B 48 O 68.7 79.1 85.6 REMARK 620 5 ASP B 50 OD1 137.2 84.5 113.5 71.0 REMARK 620 6 SER B 52 OG 140.4 111.1 94.3 150.1 81.7 REMARK 620 7 HOH B2008 O 75.6 91.8 86.5 144.4 142.9 65.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B1312 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 169 NE2 REMARK 620 2 HEM B1312 NA 88.7 REMARK 620 3 HEM B1312 NB 87.9 87.9 REMARK 620 4 HEM B1312 NC 90.9 179.0 91.2 REMARK 620 5 HEM B1312 ND 92.4 92.5 179.5 88.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1310 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 170 O REMARK 620 2 SER B 170 OG 78.1 REMARK 620 3 ASP B 223 OD2 86.5 90.4 REMARK 620 4 THR B 226 OG1 146.4 132.9 81.4 REMARK 620 5 THR B 226 O 82.8 160.8 85.8 65.2 REMARK 620 6 VAL B 229 O 89.9 93.6 174.0 99.1 89.0 REMARK 620 7 ASP B 231 OD1 139.6 63.1 103.8 73.9 136.1 82.1 REMARK 620 N 1 2 3 4 5 6 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE WAS NOT DEPOSITED IN ANY DATABASE. SEQUENCE WAS REMARK 999 OBTAINED FROM MASSPEC THOUGH. DBREF 4USC A 1 303 PDB 4USC 4USC 1 303 DBREF 4USC B 1 303 PDB 4USC 4USC 1 303 SEQRES 1 A 303 ASP LEU GLN ILE GLY PHE TYR ASN GLN SER CYS PRO SER SEQRES 2 A 303 ALA GLU SER LEU VAL GLN GLN GLY VAL ALA ALA ALA PHE SEQRES 3 A 303 ALA ASN ASN SER GLY ILE ALA PRO GLY LEU ILE ARG MET SEQRES 4 A 303 HIS PHE HIS ASP CYS PHE VAL ARG GLY CYS ASP GLY SER SEQRES 5 A 303 VAL LEU LEU ASP SER THR ASP THR ASN THR ALA GLU LYS SEQRES 6 A 303 ASP ALA ALA PRO ASN ASN PRO SER LEU ARG GLY PHE GLU SEQRES 7 A 303 VAL ILE ALA ALA ALA LYS SER ALA VAL GLU ALA ALA CYS SEQRES 8 A 303 PRO LYS THR VAL SER CYS ALA ASP ILE LEU ALA PHE ALA SEQRES 9 A 303 ALA ARG ASP SER ALA ALA LEU ALA GLY ASN ILE THR TYR SEQRES 10 A 303 GLN VAL PRO SER GLY ARG ARG ASP GLY ASN VAL SER LEU SEQRES 11 A 303 ALA SER GLU ALA LEU THR ASN ILE PRO ALA PRO THR PHE SEQRES 12 A 303 ASN ALA THR GLN LEU ILE ASN SER PHE ALA GLY LYS ASN SEQRES 13 A 303 LEU THR ALA ASP GLU MET VAL THR LEU SER GLY ALA HIS SEQRES 14 A 303 SER ILE GLY VAL SER HIS CYS PHE SER PHE LEU ASN ARG SEQRES 15 A 303 ILE TYR ASN PHE SER ASN THR SER GLN VAL ASP PRO THR SEQRES 16 A 303 LEU SER SER SER TYR ALA ASP LEU LEU ARG THR LYS CYS SEQRES 17 A 303 PRO SER ASN SER THR ARG PHE THR PRO ILE THR VAL SER SEQRES 18 A 303 LEU ASP ILE ILE THR PRO THR VAL LEU ASP ASN ARG TYR SEQRES 19 A 303 TYR THR GLY VAL GLN LEU THR LEU GLY LEU LEU THR SER SEQRES 20 A 303 ASP GLN ALA LEU VAL THR GLU ALA ASN LEU SER ALA ALA SEQRES 21 A 303 VAL LYS ASN ASN ALA ASP ASN LEU THR ALA TRP VAL ALA SEQRES 22 A 303 GLU PHE ALA GLN ALA ILE VAL LYS MET GLY GLN ILE GLU SEQRES 23 A 303 VAL LEU THR GLY THR GLN GLY GLU ILE ARG THR ASN CYS SEQRES 24 A 303 SER VAL VAL ASN SEQRES 1 B 303 ASP LEU GLN ILE GLY PHE TYR ASN GLN SER CYS PRO SER SEQRES 2 B 303 ALA GLU SER LEU VAL GLN GLN GLY VAL ALA ALA ALA PHE SEQRES 3 B 303 ALA ASN ASN SER GLY ILE ALA PRO GLY LEU ILE ARG MET SEQRES 4 B 303 HIS PHE HIS ASP CYS PHE VAL ARG GLY CYS ASP GLY SER SEQRES 5 B 303 VAL LEU LEU ASP SER THR ASP THR ASN THR ALA GLU LYS SEQRES 6 B 303 ASP ALA ALA PRO ASN ASN PRO SER LEU ARG GLY PHE GLU SEQRES 7 B 303 VAL ILE ALA ALA ALA LYS SER ALA VAL GLU ALA ALA CYS SEQRES 8 B 303 PRO LYS THR VAL SER CYS ALA ASP ILE LEU ALA PHE ALA SEQRES 9 B 303 ALA ARG ASP SER ALA ALA LEU ALA GLY ASN ILE THR TYR SEQRES 10 B 303 GLN VAL PRO SER GLY ARG ARG ASP GLY ASN VAL SER LEU SEQRES 11 B 303 ALA SER GLU ALA LEU THR ASN ILE PRO ALA PRO THR PHE SEQRES 12 B 303 ASN ALA THR GLN LEU ILE ASN SER PHE ALA GLY LYS ASN SEQRES 13 B 303 LEU THR ALA ASP GLU MET VAL THR LEU SER GLY ALA HIS SEQRES 14 B 303 SER ILE GLY VAL SER HIS CYS PHE SER PHE LEU ASN ARG SEQRES 15 B 303 ILE TYR ASN PHE SER ASN THR SER GLN VAL ASP PRO THR SEQRES 16 B 303 LEU SER SER SER TYR ALA ASP LEU LEU ARG THR LYS CYS SEQRES 17 B 303 PRO SER ASN SER THR ARG PHE THR PRO ILE THR VAL SER SEQRES 18 B 303 LEU ASP ILE ILE THR PRO THR VAL LEU ASP ASN ARG TYR SEQRES 19 B 303 TYR THR GLY VAL GLN LEU THR LEU GLY LEU LEU THR SER SEQRES 20 B 303 ASP GLN ALA LEU VAL THR GLU ALA ASN LEU SER ALA ALA SEQRES 21 B 303 VAL LYS ASN ASN ALA ASP ASN LEU THR ALA TRP VAL ALA SEQRES 22 B 303 GLU PHE ALA GLN ALA ILE VAL LYS MET GLY GLN ILE GLU SEQRES 23 B 303 VAL LEU THR GLY THR GLN GLY GLU ILE ARG THR ASN CYS SEQRES 24 B 303 SER VAL VAL ASN MODRES 4USC ASN A 8 ASN GLYCOSYLATION SITE MODRES 4USC ASN A 127 ASN GLYCOSYLATION SITE MODRES 4USC ASN A 267 ASN GLYCOSYLATION SITE MODRES 4USC ASN A 298 ASN GLYCOSYLATION SITE MODRES 4USC ASN B 8 ASN GLYCOSYLATION SITE MODRES 4USC ASN B 267 ASN GLYCOSYLATION SITE MODRES 4USC ASN B 298 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET MAN C 3 11 HET NAG D 1 14 HET FUC D 2 10 HET NAG D 3 14 HET NAG E 1 14 HET FUC E 2 10 HET NAG E 3 14 HET CA A1304 1 HET CA A1305 1 HET MAN A1309 12 HET NAG A1310 14 HET NAG A1314 14 HET NAG A1315 14 HET SO4 A1316 5 HET PEG A1317 7 HET HEM A1318 43 HET EDO A1319 4 HET PEO A1320 2 HET NAG B1307 14 HET NAG B1308 14 HET CA B1309 1 HET CA B1310 1 HET SO4 B1311 5 HET HEM B1312 43 HET EDO B1313 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM EDO 1,2-ETHANEDIOL HETNAM PEO HYDROGEN PEROXIDE 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN HEM HEME HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NAG 11(C8 H15 N O6) FORMUL 3 MAN 2(C6 H12 O6) FORMUL 4 FUC 2(C6 H12 O5) FORMUL 6 CA 4(CA 2+) FORMUL 12 SO4 2(O4 S 2-) FORMUL 13 PEG C4 H10 O3 FORMUL 14 HEM 2(C34 H32 FE N4 O4) FORMUL 15 EDO 2(C2 H6 O2) FORMUL 16 PEO H2 O2 FORMUL 24 HOH *85(H2 O) HELIX 1 1 GLY A 5 GLN A 9 5 5 HELIX 2 2 SER A 13 ASN A 29 1 17 HELIX 3 3 GLY A 31 PHE A 45 1 15 HELIX 4 4 GLY A 51 LEU A 55 5 5 HELIX 5 5 ALA A 63 ALA A 67 5 5 HELIX 6 6 GLY A 76 CYS A 91 1 16 HELIX 7 7 SER A 96 ASN A 114 1 19 HELIX 8 8 LEU A 130 ILE A 138 1 9 HELIX 9 9 ASN A 144 LYS A 155 1 12 HELIX 10 10 THR A 158 GLY A 167 1 10 HELIX 11 11 ALA A 168 ILE A 171 5 4 HELIX 12 12 CYS A 176 LEU A 180 1 5 HELIX 13 13 ASN A 181 ILE A 183 5 3 HELIX 14 14 SER A 197 CYS A 208 1 12 HELIX 15 15 ASN A 232 LEU A 240 1 9 HELIX 16 16 LEU A 245 ALA A 250 1 6 HELIX 17 17 LEU A 251 THR A 253 5 3 HELIX 18 18 GLU A 254 ASN A 267 1 14 HELIX 19 19 ASN A 267 GLY A 283 1 17 HELIX 20 20 PHE B 6 GLN B 9 5 4 HELIX 21 21 SER B 13 ASN B 29 1 17 HELIX 22 22 GLY B 31 PHE B 45 1 15 HELIX 23 23 GLY B 51 LEU B 55 5 5 HELIX 24 24 ALA B 63 ALA B 67 5 5 HELIX 25 25 GLY B 76 CYS B 91 1 16 HELIX 26 26 SER B 96 ASN B 114 1 19 HELIX 27 27 LEU B 130 ILE B 138 1 9 HELIX 28 28 ASN B 144 LYS B 155 1 12 HELIX 29 29 THR B 158 GLY B 167 1 10 HELIX 30 30 ALA B 168 ILE B 171 5 4 HELIX 31 31 CYS B 176 LEU B 180 1 5 HELIX 32 32 ASN B 181 ILE B 183 5 3 HELIX 33 33 SER B 197 CYS B 208 1 12 HELIX 34 34 ASN B 232 LEU B 240 1 9 HELIX 35 35 LEU B 245 ALA B 250 1 6 HELIX 36 36 LEU B 251 THR B 253 5 3 HELIX 37 37 GLU B 254 ASN B 267 1 14 HELIX 38 38 ASN B 267 GLY B 283 1 17 SHEET 1 AA 2 VAL A 173 HIS A 175 0 SHEET 2 AA 2 THR A 219 SER A 221 -1 O VAL A 220 N SER A 174 SHEET 1 BA 2 GLN B 3 ILE B 4 0 SHEET 2 BA 2 PRO B 120 SER B 121 -1 O SER B 121 N GLN B 3 SHEET 1 BB 2 VAL B 173 HIS B 175 0 SHEET 2 BB 2 THR B 219 SER B 221 -1 O VAL B 220 N SER B 174 SSBOND 1 CYS A 11 CYS A 91 1555 1555 2.01 SSBOND 2 CYS A 44 CYS A 49 1555 1555 2.09 SSBOND 3 CYS A 97 CYS A 299 1555 1555 2.11 SSBOND 4 CYS A 176 CYS A 208 1555 1555 2.10 SSBOND 5 CYS B 11 CYS B 91 1555 1555 2.01 SSBOND 6 CYS B 44 CYS B 49 1555 1555 2.07 SSBOND 7 CYS B 97 CYS B 299 1555 1555 2.12 SSBOND 8 CYS B 176 CYS B 208 1555 1555 2.06 LINK ND2 ASN A 8 C1 NAG A1310 1555 1555 1.47 LINK ND2 ASN A 127 C1 NAG A1314 1555 1555 1.38 LINK ND2 ASN A 267 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN A 298 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN B 8 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN B 267 C1 NAG B1307 1555 1555 1.45 LINK ND2 ASN B 298 C1 NAG B1308 1555 1555 1.45 LINK O3 NAG C 1 C1 NAG C 2 1555 1555 1.47 LINK O4 NAG C 2 C1 MAN C 3 1555 1555 1.45 LINK O3 NAG D 1 C1 FUC D 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 3 1555 1555 1.44 LINK O3 NAG E 1 C1 FUC E 2 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 3 1555 1555 1.45 LINK OD1 ASP A 43 CA CA A1305 1555 1555 2.28 LINK O ASP A 43 CA CA A1305 1555 1555 2.57 LINK O VAL A 46 CA CA A1305 1555 1555 2.27 LINK O GLY A 48 CA CA A1305 1555 1555 2.52 LINK OD1 ASP A 50 CA CA A1305 1555 1555 2.34 LINK OG SER A 52 CA CA A1305 1555 1555 2.45 LINK NE2 HIS A 169 FE HEM A1318 1555 1555 2.09 LINK OG SER A 170 CA CA A1304 1555 1555 2.41 LINK O SER A 170 CA CA A1304 1555 1555 2.35 LINK OD2 ASP A 223 CA CA A1304 1555 1555 2.24 LINK OG1 THR A 226 CA CA A1304 1555 1555 2.31 LINK O THR A 226 CA CA A1304 1555 1555 2.59 LINK O VAL A 229 CA CA A1304 1555 1555 2.23 LINK OD1 ASP A 231 CA CA A1304 1555 1555 2.64 LINK CA CA A1305 O HOH A2009 1555 1555 2.49 LINK FE HEM A1318 O1 PEO A1320 1555 1555 2.33 LINK O ASP B 43 CA CA B1309 1555 1555 2.62 LINK OD1 ASP B 43 CA CA B1309 1555 1555 2.35 LINK O VAL B 46 CA CA B1309 1555 1555 2.29 LINK O GLY B 48 CA CA B1309 1555 1555 2.53 LINK OD1 ASP B 50 CA CA B1309 1555 1555 2.35 LINK OG SER B 52 CA CA B1309 1555 1555 2.39 LINK NE2 HIS B 169 FE HEM B1312 1555 1555 2.14 LINK O SER B 170 CA CA B1310 1555 1555 2.40 LINK OG SER B 170 CA CA B1310 1555 1555 2.52 LINK OD2 ASP B 223 CA CA B1310 1555 1555 2.30 LINK OG1 THR B 226 CA CA B1310 1555 1555 2.29 LINK O THR B 226 CA CA B1310 1555 1555 2.49 LINK O VAL B 229 CA CA B1310 1555 1555 2.19 LINK OD1 ASP B 231 CA CA B1310 1555 1555 2.74 LINK CA CA B1309 O HOH B2008 1555 1555 2.56 CISPEP 1 ASN A 71 PRO A 72 0 16.72 CISPEP 2 ASN B 71 PRO B 72 0 13.21 CRYST1 70.180 100.650 132.310 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 0.014249 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007558 0.00000 MTRIX1 1 -1.000000 -0.008300 -0.000100 -0.00530 1 MTRIX2 1 -0.008300 0.999900 -0.011200 0.12260 1 MTRIX3 1 0.000200 -0.011200 -0.999900 15.97510 1