HEADER OXIDOREDUCTASE 16-NOV-16 5MEW TITLE THE STUDY OF THE X-RAY INDUCED ENZYMATIC REDUCTION OF MOLECULAR OXYGEN TITLE 2 TO WATER FOR LACCASE FROM STECCHERINUM MURASHKINSKYI. SECOND TITLE 3 STRUCTURE OF THE SERIES WITH TOTAL EXPOSITION TIME 33 MIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACCASE 2; COMPND 3 CHAIN: A; COMPND 4 EC: 1.10.3.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STECCHERINUM MURASHKINSKYI; SOURCE 3 ORGANISM_TAXID: 627145 KEYWDS MOLECULAR OXYGEN MULTI COPPER OXIDASE, LACCASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.POLYAKOV,T.N.FEDOROVA,S.GAVRYUSHOV,A.N.POPOV,O.A.GLAZUNOVA REVDAT 7 16-OCT-24 5MEW 1 REMARK REVDAT 6 17-JAN-24 5MEW 1 HETSYN REVDAT 5 29-JUL-20 5MEW 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 17-JUL-19 5MEW 1 REMARK REVDAT 3 31-JAN-18 5MEW 1 REMARK REVDAT 2 24-MAY-17 5MEW 1 JRNL REVDAT 1 10-MAY-17 5MEW 0 JRNL AUTH K.M.POLYAKOV,S.GAVRYUSHOV,S.IVANOVA,T.V.FEDOROVA, JRNL AUTH 2 O.A.GLAZUNOVA,A.N.POPOV,O.V.KOROLEVA JRNL TITL STRUCTURAL STUDY OF THE X-RAY-INDUCED ENZYMATIC REDUCTION OF JRNL TITL 2 MOLECULAR OXYGEN TO WATER BY STECCHERINUM MURASHKINSKYI JRNL TITL 3 LACCASE: INSIGHTS INTO THE REACTION MECHANISM. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 388 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28471364 JRNL DOI 10.1107/S2059798317003667 REMARK 2 REMARK 2 RESOLUTION. 1.35 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 111218 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5868 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8003 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 474 REMARK 3 BIN FREE R VALUE : 0.2070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3775 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 718 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.10000 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): 0.041 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.643 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4152 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3333 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5703 ; 2.032 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7668 ; 0.914 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 516 ; 7.267 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;36.444 ;25.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 552 ;11.098 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;20.780 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 658 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4697 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 876 ; 0.001 ; 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): 2052 ; 1.062 ; 0.945 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2035 ; 0.986 ; 0.926 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2570 ; 1.563 ; 1.420 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2552 ; 1.456 ; 1.395 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2100 ; 1.579 ;54.802 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1990 ; 1.496 ;57.718 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2974 ; 2.238 ; 1.479 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5149 ; 4.735 ; 9.614 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4540 ; 4.012 ; 8.080 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): 6 ; 3.742 ; 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5MEW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.81230 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 117126 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.29600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5E9N REMARK 200 REMARK 200 REMARK: THE CRYSTAL IS A TETRAGONAL PRISM WITH REMARK 200 DIMENSION 0.3 X 0.2 X 0.15 MM. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION (12MG/ML, 002M K REMARK 280 -PHOSPHATE BUFFER, PH 6.5). RESERVOIR SOLUTION 0.1M CITRATE- REMARK 280 PHOSPHATE BUFFER PH4.0, 0.2M AMMONIUM ACETATE, 25% PEG 4000, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 28.19000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.24500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.24500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.19000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.20000 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 TOTAL BURIED SURFACE AREA: 2400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 HD21 ASN A 436 C1 NAG B 1 0.50 REMARK 500 HD21 ASN A 414 C1 NAG C 1 0.53 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 CG2 THR A 295 O HOH A 1026 4555 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 377 CB SER A 377 OG -0.105 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 198 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 200 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 202 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 209 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 237 CB - CG - OD1 ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 263 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LEU A 59 129.32 78.96 REMARK 500 PHE A 107 -169.99 -127.63 REMARK 500 SER A 114 -135.83 49.82 REMARK 500 ASP A 142 -167.60 -160.74 REMARK 500 ASP A 209 -70.96 -161.22 REMARK 500 ALA A 244 -8.04 83.42 REMARK 500 VAL A 420 -62.82 -109.74 REMARK 500 ASN A 421 39.32 -143.18 REMARK 500 ASN A 436 59.67 -144.33 REMARK 500 ASN A 444 32.37 -140.41 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 A1318 DISTANCE = 6.05 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 CU A 503 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 65 NE2 REMARK 620 2 HIS A 400 NE2 173.9 REMARK 620 3 HOH A 605 O 85.0 89.0 REMARK 620 4 HOH A 929 O 93.5 92.6 177.7 REMARK 620 5 HOH A1005 O 90.7 95.4 175.6 3.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 HIS A 110 NE2 110.9 REMARK 620 3 HIS A 454 NE2 98.5 103.4 REMARK 620 4 OXY A 511 O1 127.9 109.1 103.2 REMARK 620 5 OXY A 511 O2 155.8 91.7 83.9 30.2 REMARK 620 6 HOH A 605 O 91.4 118.6 129.8 39.5 69.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 HIS A 110 NE2 144.0 REMARK 620 3 HIS A 454 NE2 105.4 110.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 112 NE2 REMARK 620 2 HIS A 402 NE2 94.1 REMARK 620 3 HIS A 452 NE2 107.9 99.4 REMARK 620 4 OXY A 511 O2 91.9 163.1 93.7 REMARK 620 5 HOH A 605 O 128.1 88.3 122.8 75.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 501 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 112 NE2 REMARK 620 2 HIS A 402 NE2 105.8 REMARK 620 3 HIS A 452 NE2 135.1 115.7 REMARK 620 4 OXY A 511 O1 98.0 97.0 93.3 REMARK 620 5 OXY A 511 O2 83.0 125.6 86.2 29.5 REMARK 620 6 HOH A 605 O 89.4 111.3 90.8 15.1 14.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 514 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 317 O REMARK 620 2 HOH A 815 O 85.6 REMARK 620 3 HOH A1074 O 94.2 155.4 REMARK 620 4 HOH A1078 O 86.6 164.7 38.6 REMARK 620 5 HOH A1116 O 72.6 84.5 72.1 105.7 REMARK 620 6 HOH A1125 O 78.9 85.8 118.3 79.8 150.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 504 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 397 ND1 REMARK 620 2 CYS A 453 SG 125.0 REMARK 620 3 HIS A 458 ND1 103.1 131.4 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5E9N RELATED DB: PDB DBREF 5MEW A 1 498 UNP I1VE66 I1VE66_9APHY 20 517 SEQADV 5MEW ALA A 499 UNP I1VE66 EXPRESSION TAG SEQRES 1 A 499 ALA GLN ILE GLY PRO VAL THR ASP LEU HIS ILE THR ASN SEQRES 2 A 499 ALA ASN ILE SER PRO ASP GLY PHE SER ARG PRO ALA VAL SEQRES 3 A 499 LEU ALA GLY GLY THR PHE PRO GLY PRO THR ILE ALA GLY SEQRES 4 A 499 ASN THR GLY ASP ASN PHE GLN ILE THR VAL PHE ASN ASP SEQRES 5 A 499 LEU THR ASP PRO SER MET LEU THR ASP THR SER ILE HIS SEQRES 6 A 499 TRP HIS GLY LEU PHE GLN LYS GLY THR ASN TRP ALA ASP SEQRES 7 A 499 GLY PRO ALA PHE VAL THR GLN CYS PRO ILE ILE THR GLY SEQRES 8 A 499 GLN SER PHE ASP TYR ASN PHE ASN VAL PRO GLY GLN ALA SEQRES 9 A 499 GLY THR PHE TRP TYR HIS SER HIS LEU SER THR GLN TYR SEQRES 10 A 499 CYS ASP GLY LEU ARG GLY PRO PHE VAL VAL TYR ASP PRO SEQRES 11 A 499 ASN ASP PRO ASN ALA SER LEU TYR ASP VAL ASP ASP ASP SEQRES 12 A 499 THR THR ILE ILE THR LEU ALA ASP TRP TYR HIS THR LEU SEQRES 13 A 499 ALA GLN GLN GLU PRO ILE GLY ALA ALA ILE THR ALA ASP SEQRES 14 A 499 ALA THR LEU ILE ASN GLY LEU GLY ARG SER PHE THR ASN SEQRES 15 A 499 THR THR ALA SER PRO LEU SER VAL ILE THR VAL GLN SER SEQRES 16 A 499 GLY LYS ARG TYR ARG MET ARG LEU VAL SER ILE SER CYS SEQRES 17 A 499 ASP PRO ASN TYR LEU PHE SER ILE ASP GLY HIS ASP MET SEQRES 18 A 499 THR ILE ILE GLU VAL ASP GLY VAL ASN SER GLN GLN LEU SEQRES 19 A 499 THR VAL ASP GLN ILE GLN ILE PHE ALA ALA GLN ARG TYR SEQRES 20 A 499 SER PHE VAL LEU ASN ALA ASN GLN PRO VAL GLY ASN TYR SEQRES 21 A 499 TRP ILE ARG ALA GLN PRO ASN SER GLY GLY GLN GLY PHE SEQRES 22 A 499 ASP GLY GLY ILE ASN SER ALA ILE LEU ARG TYR GLU GLY SEQRES 23 A 499 ALA THR VAL GLU ASP PRO THR THR THR ALA PRO THR THR SEQRES 24 A 499 PHE SER ASN PRO LEU VAL GLU THR ASP LEU HIS PRO LEU SEQRES 25 A 499 ALA ASP LEU GLY VAL PRO GLY GLN PRO PHE ARG GLY GLY SEQRES 26 A 499 ALA ASP ASP PRO LEU VAL LEU ASN LEU ALA PHE ALA ASN SEQRES 27 A 499 GLY ARG PHE SER ILE ASP GLY VAL SER PHE VAL PRO PRO SEQRES 28 A 499 THR VAL PRO VAL LEU LEU GLN ILE LEU SER GLY ALA GLN SEQRES 29 A 499 ASN ALA GLN ASP LEU LEU PRO ALA GLY SER VAL ILE SER SEQRES 30 A 499 LEU PRO SER ASN SER VAL ILE GLU VAL ALA LEU PRO ALA SEQRES 31 A 499 GLY ALA ALA GLY GLY PRO HIS PRO PHE HIS LEU HIS GLY SEQRES 32 A 499 HIS ASN PHE ALA VAL VAL GLN SER ALA ASN ASN ALA THR SEQRES 33 A 499 PRO ASN TYR VAL ASN PRO ILE TRP ARG ASP THR VAL SER SEQRES 34 A 499 ILE GLY GLY THR GLY ASP ASN VAL THR ILE ARG PHE THR SEQRES 35 A 499 THR ASN ASN PRO GLY PRO TRP PHE LEU HIS CYS HIS ILE SEQRES 36 A 499 ASP TRP HIS LEU GLU ALA GLY PHE ALA ILE VAL PHE ALA SEQRES 37 A 499 GLU ASP ILE PRO ASP THR ALA SER ALA ASN PRO VAL PRO SEQRES 38 A 499 GLN ALA TRP SER ASP LEU CYS PRO ALA TYR ASP GLN ALA SEQRES 39 A 499 HIS ASN ILE SER ALA MODRES 5MEW NAG B 1 NAG -D MODRES 5MEW NAG C 1 NAG -D MODRES 5MEW NAG C 2 NAG -D MODRES 5MEW NAG B 2 NAG -D HET NAG B 1 14 HET NAG B 2 18 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET CU A 501 2 HET CU A 502 2 HET CU A 503 1 HET CU A 504 1 HET OXY A 511 2 HET OXY A 512 2 HET CIT A 513 13 HET NA A 514 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM CU COPPER (II) ION HETNAM OXY OXYGEN MOLECULE HETNAM CIT CITRIC ACID HETNAM NA SODIUM ION 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 BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 4 CU 4(CU 2+) FORMUL 8 OXY 2(O2) FORMUL 10 CIT C6 H8 O7 FORMUL 11 NA NA 1+ FORMUL 12 HOH *718(H2 O) HELIX 1 AA1 ASP A 55 LEU A 59 5 5 HELIX 2 AA2 THR A 74 ASP A 78 5 5 HELIX 3 AA3 THR A 115 GLY A 120 5 6 HELIX 4 AA4 ASN A 134 TYR A 138 5 5 HELIX 5 AA5 ASP A 142 THR A 144 5 3 HELIX 6 AA6 LEU A 156 GLU A 160 5 5 HELIX 7 AA7 PHE A 273 ILE A 277 5 5 HELIX 8 AA8 VAL A 305 LEU A 309 5 5 HELIX 9 AA9 PRO A 354 SER A 361 1 8 HELIX 10 AB1 ASN A 365 LEU A 369 5 5 HELIX 11 AB2 ILE A 455 ALA A 461 1 7 HELIX 12 AB3 ASP A 473 ASN A 478 1 6 HELIX 13 AB4 PRO A 481 HIS A 495 1 15 SHEET 1 AA1 4 ARG A 23 ALA A 28 0 SHEET 2 AA1 4 VAL A 6 ILE A 16 -1 N THR A 12 O LEU A 27 SHEET 3 AA1 4 ASN A 44 ASN A 51 1 O PHE A 50 N ILE A 11 SHEET 4 AA1 4 SER A 93 ASN A 99 -1 O PHE A 94 N VAL A 49 SHEET 1 AA2 4 ILE A 37 ASN A 40 0 SHEET 2 AA2 4 ARG A 122 TYR A 128 1 O TYR A 128 N GLY A 39 SHEET 3 AA2 4 GLY A 105 SER A 111 -1 N TYR A 109 O GLY A 123 SHEET 4 AA2 4 ILE A 64 HIS A 67 -1 N HIS A 65 O HIS A 110 SHEET 1 AA3 6 ALA A 170 ILE A 173 0 SHEET 2 AA3 6 ILE A 146 TRP A 152 -1 N ALA A 150 O LEU A 172 SHEET 3 AA3 6 ARG A 198 SER A 205 1 O VAL A 204 N ILE A 147 SHEET 4 AA3 6 ARG A 246 ASN A 252 -1 O TYR A 247 N LEU A 203 SHEET 5 AA3 6 MET A 221 VAL A 226 -1 N THR A 222 O VAL A 250 SHEET 6 AA3 6 VAL A 229 VAL A 236 -1 O LEU A 234 N ILE A 223 SHEET 1 AA4 5 VAL A 190 VAL A 193 0 SHEET 2 AA4 5 SER A 279 TYR A 284 1 O ARG A 283 N ILE A 191 SHEET 3 AA4 5 ASN A 259 PRO A 266 -1 N TYR A 260 O LEU A 282 SHEET 4 AA4 5 TYR A 212 ILE A 216 -1 N SER A 215 O ARG A 263 SHEET 5 AA4 5 ILE A 239 ILE A 241 -1 O ILE A 239 N PHE A 214 SHEET 1 AA5 5 ASP A 328 VAL A 331 0 SHEET 2 AA5 5 VAL A 383 ALA A 387 1 O GLU A 385 N LEU A 330 SHEET 3 AA5 5 THR A 438 THR A 442 -1 O PHE A 441 N ILE A 384 SHEET 4 AA5 5 PHE A 406 GLN A 410 -1 N ALA A 407 O ARG A 440 SHEET 5 AA5 5 TRP A 424 ARG A 425 -1 O ARG A 425 N PHE A 406 SHEET 1 AA6 2 LEU A 334 ALA A 337 0 SHEET 2 AA6 2 ARG A 340 ILE A 343 -1 O SER A 342 N ALA A 335 SHEET 1 AA7 5 VAL A 375 LEU A 378 0 SHEET 2 AA7 5 ALA A 464 GLU A 469 1 O VAL A 466 N ILE A 376 SHEET 3 AA7 5 GLY A 447 CYS A 453 -1 N TRP A 449 O PHE A 467 SHEET 4 AA7 5 PRO A 398 LEU A 401 -1 N HIS A 400 O HIS A 452 SHEET 5 AA7 5 THR A 427 SER A 429 -1 O VAL A 428 N PHE A 399 SSBOND 1 CYS A 86 CYS A 488 1555 1555 2.06 SSBOND 2 CYS A 118 CYS A 208 1555 1555 2.03 LINK ND2 ASN A 414 C1 NAG C 1 1555 1555 1.48 LINK ND2 ASN A 436 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.47 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.41 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK NE2 HIS A 65 CU CU A 503 1555 1555 1.90 LINK ND1 HIS A 67 CU A CU A 502 1555 1555 2.16 LINK ND1 HIS A 67 CU B CU A 502 1555 1555 1.86 LINK NE2 HIS A 110 CU A CU A 502 1555 1555 2.23 LINK NE2 HIS A 110 CU B CU A 502 1555 1555 1.94 LINK NE2 HIS A 112 CU A CU A 501 1555 1555 2.17 LINK NE2 HIS A 112 CU B CU A 501 1555 1555 1.93 LINK O VAL A 317 NA NA A 514 1555 1555 2.37 LINK ND1 HIS A 397 CU CU A 504 1555 1555 2.00 LINK NE2 HIS A 400 CU CU A 503 1555 1555 1.91 LINK NE2 HIS A 402 CU A CU A 501 1555 1555 2.06 LINK NE2 HIS A 402 CU B CU A 501 1555 1555 1.95 LINK NE2 HIS A 452 CU A CU A 501 1555 1555 2.18 LINK NE2 HIS A 452 CU B CU A 501 1555 1555 1.87 LINK SG CYS A 453 CU CU A 504 1555 1555 2.17 LINK NE2 HIS A 454 CU A CU A 502 1555 1555 2.03 LINK NE2 HIS A 454 CU B CU A 502 1555 1555 2.12 LINK ND1 HIS A 458 CU CU A 504 1555 1555 2.01 LINK CU A CU A 501 O2 OXY A 511 1555 1555 1.92 LINK CU B CU A 501 O1 OXY A 511 1555 1555 2.24 LINK CU B CU A 501 O2 OXY A 511 1555 1555 2.47 LINK CU A CU A 501 O AHOH A 605 1555 1555 2.37 LINK CU B CU A 501 O BHOH A 605 1555 1555 2.51 LINK CU A CU A 502 O1 OXY A 511 1555 1555 2.14 LINK CU A CU A 502 O2 OXY A 511 1555 1555 2.42 LINK CU A CU A 502 O AHOH A 605 1555 1555 2.22 LINK CU CU A 503 O AHOH A 605 1555 1555 1.84 LINK CU CU A 503 O HOH A 929 1555 1555 2.03 LINK CU CU A 503 O HOH A1005 1555 1555 2.63 LINK NA NA A 514 O HOH A 815 1555 1555 2.32 LINK NA NA A 514 O HOH A1074 1555 1555 2.01 LINK NA NA A 514 O HOH A1078 1555 1555 2.50 LINK NA NA A 514 O HOH A1116 1555 1555 2.87 LINK NA NA A 514 O HOH A1125 1555 1555 2.63 CISPEP 1 GLY A 4 PRO A 5 0 6.52 CISPEP 2 PHE A 32 PRO A 33 0 -14.54 CISPEP 3 LEU A 370 PRO A 371 0 3.26 CISPEP 4 GLY A 395 PRO A 396 0 1.93 CRYST1 56.380 84.400 112.490 90.00 90.00 90.00 P 21 21 21 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 0.017737 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008890 0.00000