HEADER OXIDOREDUCTASE 28-NOV-16 5MIB TITLE THE STUDY OF THE X-RAY INDUCED ENZYMATIC REDUCTION OF MOLECULAR OXYGEN TITLE 2 TO WATER FOR LACCASE FROM STECCHERINUM MURASHKINSKYI.THE 12-TH TITLE 3 STRUCTURE OF THE SERIES WITH TOTAL EXPOSITION TIME 333 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 MULTI COPPER OXIDASE, LACCASE, COMPLEX WITH MOLECULAR OXYGEN, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.POLYAKOV,S.GAVRYUSHOV,T.V.FEDOROVA,O.A.GLAZUNOVA,A.N.POPOV REVDAT 5 17-JAN-24 5MIB 1 HETSYN REVDAT 4 29-JUL-20 5MIB 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 17-JUL-19 5MIB 1 REMARK REVDAT 2 24-MAY-17 5MIB 1 JRNL REVDAT 1 10-MAY-17 5MIB 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) : 67.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 110288 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) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.148 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5823 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) : 8215 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 437 REMARK 3 BIN FREE R VALUE : 0.2150 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 : 78 REMARK 3 SOLVENT ATOMS : 707 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.09000 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): 0.042 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.626 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4116 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3312 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5647 ; 1.969 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7621 ; 0.907 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 514 ; 7.152 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;36.931 ;25.208 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 552 ;11.139 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 642 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4677 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 871 ; 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): 2044 ; 1.063 ; 0.963 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2027 ; 1.022 ; 0.944 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2559 ; 1.571 ; 1.447 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2541 ; 1.495 ; 1.422 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2072 ; 1.684 ;37.569 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1990 ; 1.602 ;39.034 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2971 ; 2.354 ; 1.511 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5064 ; 4.762 ; 9.693 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4501 ; 4.093 ; 8.262 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 ; 8.145 ; 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 5MIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-NOV-16. REMARK 100 THE DEPOSITION ID IS D_1200002503. 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 : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116112 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 67.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2900 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.530 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: 5MEW 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 ACETAT, 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 28.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.25500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.22500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.25500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.22500 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: 2160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18010 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -18 REMARK 465 ALA A -17 REMARK 465 SER A -16 REMARK 465 PHE A -15 REMARK 465 LYS A -14 REMARK 465 SER A -13 REMARK 465 ILE A -12 REMARK 465 ALA A -11 REMARK 465 ALA A -10 REMARK 465 LEU A -9 REMARK 465 ILE A -8 REMARK 465 ALA A -7 REMARK 465 LEU A -6 REMARK 465 ILE A -5 REMARK 465 PHE A -4 REMARK 465 ALA A -3 REMARK 465 VAL A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 ALA A 500 REMARK 465 THR A 501 REMARK 465 ARG A 502 REMARK 465 GLN A 503 REMARK 465 ASP A 504 REMARK 465 PHE A 505 REMARK 465 GLN A 506 REMARK 465 ILE A 507 REMARK 465 LEU A 508 REMARK 465 CYS A 509 REMARK 465 ILE A 510 REMARK 465 CYS A 511 REMARK 465 GLY A 512 REMARK 465 ILE A 513 REMARK 465 LEU A 514 REMARK 465 HIS A 515 REMARK 465 VAL A 516 REMARK 465 ASN A 517 REMARK 465 PHE A 518 REMARK 465 ARG A 519 REMARK 465 GLN A 520 REMARK 465 GLU A 521 REMARK 465 GLU A 522 REMARK 465 ARG A 523 REMARK 465 CYS A 524 REMARK 465 GLY A 525 REMARK 465 ILE A 526 REMARK 465 SER A 527 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 THR A 499 OG1 CG2 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 O HOH A 715 O HOH A 1335 2.13 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 -0.117 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 95 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 169 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 198 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 198 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP A 209 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 237 CB - CG - OD1 ANGL. DEV. = 9.8 DEGREES REMARK 500 ASP A 327 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 VAL A 409 CA - CB - CG2 ANGL. DEV. = 10.1 DEGREES REMARK 500 PHE A 450 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 PHE A 450 CB - CG - CD1 ANGL. DEV. = 4.2 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 59 129.60 77.87 REMARK 500 PHE A 107 -169.21 -128.24 REMARK 500 SER A 114 -138.48 49.60 REMARK 500 ASP A 209 -70.67 -161.87 REMARK 500 ALA A 244 -7.09 83.28 REMARK 500 ALA A 393 152.24 -49.79 REMARK 500 VAL A 420 -64.17 -109.44 REMARK 500 ASN A 421 39.79 -144.28 REMARK 500 ASN A 436 58.07 -144.10 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 HIS A 404 ASN A 405 149.45 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 A1407 DISTANCE = 6.07 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 603 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 65 NE2 REMARK 620 2 HIS A 400 NE2 174.7 REMARK 620 3 HOH A 705 O 84.3 90.4 REMARK 620 4 HOH A1029 O 92.5 92.8 176.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 602 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 HIS A 110 NE2 125.7 REMARK 620 3 HIS A 454 NE2 104.6 104.2 REMARK 620 4 OXY A 609 O1 123.6 100.7 91.2 REMARK 620 5 HOH A 704 O 122.3 103.9 87.7 4.2 REMARK 620 6 HOH A 705 O 94.8 116.5 110.3 30.6 31.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 602 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 HIS A 110 NE2 139.6 REMARK 620 3 HIS A 454 NE2 110.0 108.2 REMARK 620 4 OXY A 609 O1 109.2 89.6 80.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 601 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 112 NE2 REMARK 620 2 HIS A 402 NE2 101.2 REMARK 620 3 HIS A 452 NE2 108.6 109.2 REMARK 620 4 OXY A 609 O1 106.1 113.3 117.0 REMARK 620 5 OXY A 609 O2 89.6 146.1 97.2 33.1 REMARK 620 6 HOH A 704 O 109.6 114.8 112.6 4.6 32.4 REMARK 620 7 HOH A 705 O 120.3 85.2 125.1 28.9 61.8 29.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 601 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 112 NE2 REMARK 620 2 HIS A 402 NE2 110.2 REMARK 620 3 HIS A 452 NE2 123.1 123.4 REMARK 620 4 OXY A 609 O1 90.8 95.4 101.1 REMARK 620 5 OXY A 609 O2 79.6 121.4 87.5 26.2 REMARK 620 6 HOH A 701 O 89.3 106.3 92.7 11.2 15.9 REMARK 620 7 HOH A 704 O 93.6 96.5 97.7 3.5 25.7 9.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 612 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 317 O REMARK 620 2 HOH A 939 O 85.7 REMARK 620 3 HOH A1175 O 93.7 153.5 REMARK 620 4 HOH A1177 O 86.6 165.5 39.5 REMARK 620 5 HOH A1196 O 76.2 92.8 61.5 97.3 REMARK 620 6 HOH A1215 O 79.4 86.6 119.4 79.8 155.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 604 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 397 ND1 REMARK 620 2 CYS A 453 SG 122.4 REMARK 620 3 HIS A 458 ND1 105.1 132.2 REMARK 620 N 1 2 DBREF 5MIB A -18 527 UNP I1VE66 I1VE66_9APHY 1 546 SEQRES 1 A 546 MET ALA SER PHE LYS SER ILE ALA ALA LEU ILE ALA LEU SEQRES 2 A 546 ILE PHE ALA VAL ASN ALA ALA GLN ILE GLY PRO VAL THR SEQRES 3 A 546 ASP LEU HIS ILE THR ASN ALA ASN ILE SER PRO ASP GLY SEQRES 4 A 546 PHE SER ARG PRO ALA VAL LEU ALA GLY GLY THR PHE PRO SEQRES 5 A 546 GLY PRO THR ILE ALA GLY ASN THR GLY ASP ASN PHE GLN SEQRES 6 A 546 ILE THR VAL PHE ASN ASP LEU THR ASP PRO SER MET LEU SEQRES 7 A 546 THR ASP THR SER ILE HIS TRP HIS GLY LEU PHE GLN LYS SEQRES 8 A 546 GLY THR ASN TRP ALA ASP GLY PRO ALA PHE VAL THR GLN SEQRES 9 A 546 CYS PRO ILE ILE THR GLY GLN SER PHE ASP TYR ASN PHE SEQRES 10 A 546 ASN VAL PRO GLY GLN ALA GLY THR PHE TRP TYR HIS SER SEQRES 11 A 546 HIS LEU SER THR GLN TYR CYS ASP GLY LEU ARG GLY PRO SEQRES 12 A 546 PHE VAL VAL TYR ASP PRO ASN ASP PRO ASN ALA SER LEU SEQRES 13 A 546 TYR ASP VAL ASP ASP ASP THR THR ILE ILE THR LEU ALA SEQRES 14 A 546 ASP TRP TYR HIS THR LEU ALA GLN GLN GLU PRO ILE GLY SEQRES 15 A 546 ALA ALA ILE THR ALA ASP ALA THR LEU ILE ASN GLY LEU SEQRES 16 A 546 GLY ARG SER PHE THR ASN THR THR ALA SER PRO LEU SER SEQRES 17 A 546 VAL ILE THR VAL GLN SER GLY LYS ARG TYR ARG MET ARG SEQRES 18 A 546 LEU VAL SER ILE SER CYS ASP PRO ASN TYR LEU PHE SER SEQRES 19 A 546 ILE ASP GLY HIS ASP MET THR ILE ILE GLU VAL ASP GLY SEQRES 20 A 546 VAL ASN SER GLN GLN LEU THR VAL ASP GLN ILE GLN ILE SEQRES 21 A 546 PHE ALA ALA GLN ARG TYR SER PHE VAL LEU ASN ALA ASN SEQRES 22 A 546 GLN PRO VAL GLY ASN TYR TRP ILE ARG ALA GLN PRO ASN SEQRES 23 A 546 SER GLY GLY GLN GLY PHE ASP GLY GLY ILE ASN SER ALA SEQRES 24 A 546 ILE LEU ARG TYR GLU GLY ALA THR VAL GLU ASP PRO THR SEQRES 25 A 546 THR THR ALA PRO THR THR PHE SER ASN PRO LEU VAL GLU SEQRES 26 A 546 THR ASP LEU HIS PRO LEU ALA ASP LEU GLY VAL PRO GLY SEQRES 27 A 546 GLN PRO PHE ARG GLY GLY ALA ASP ASP PRO LEU VAL LEU SEQRES 28 A 546 ASN LEU ALA PHE ALA ASN GLY ARG PHE SER ILE ASP GLY SEQRES 29 A 546 VAL SER PHE VAL PRO PRO THR VAL PRO VAL LEU LEU GLN SEQRES 30 A 546 ILE LEU SER GLY ALA GLN ASN ALA GLN ASP LEU LEU PRO SEQRES 31 A 546 ALA GLY SER VAL ILE SER LEU PRO SER ASN SER VAL ILE SEQRES 32 A 546 GLU VAL ALA LEU PRO ALA GLY ALA ALA GLY GLY PRO HIS SEQRES 33 A 546 PRO PHE HIS LEU HIS GLY HIS ASN PHE ALA VAL VAL GLN SEQRES 34 A 546 SER ALA ASN ASN ALA THR PRO ASN TYR VAL ASN PRO ILE SEQRES 35 A 546 TRP ARG ASP THR VAL SER ILE GLY GLY THR GLY ASP ASN SEQRES 36 A 546 VAL THR ILE ARG PHE THR THR ASN ASN PRO GLY PRO TRP SEQRES 37 A 546 PHE LEU HIS CYS HIS ILE ASP TRP HIS LEU GLU ALA GLY SEQRES 38 A 546 PHE ALA ILE VAL PHE ALA GLU ASP ILE PRO ASP THR ALA SEQRES 39 A 546 SER ALA ASN PRO VAL PRO GLN ALA TRP SER ASP LEU CYS SEQRES 40 A 546 PRO ALA TYR ASP GLN ALA HIS ASN ILE SER THR ALA THR SEQRES 41 A 546 ARG GLN ASP PHE GLN ILE LEU CYS ILE CYS GLY ILE LEU SEQRES 42 A 546 HIS VAL ASN PHE ARG GLN GLU GLU ARG CYS GLY ILE SER MODRES 5MIB NAG B 1 NAG -D MODRES 5MIB NAG C 1 NAG -D MODRES 5MIB NAG C 2 NAG -D MODRES 5MIB NAG B 2 NAG -D HET NAG B 1 14 HET NAG B 2 14 HET NAG C 1 14 HET NAG C 2 14 HET CU A 601 2 HET CU A 602 2 HET CU A 603 1 HET CU A 604 1 HET OXY A 609 2 HET OXY A 610 2 HET CIT A 611 13 HET NA A 612 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 2 NAG 4(C8 H15 N 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 *707(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 ASP A 486 1 6 HELIX 14 AB5 ASP A 486 HIS A 495 1 10 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 ILE A 281 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 2.14 SSBOND 2 CYS A 118 CYS A 208 1555 1555 2.04 LINK ND2 ASN A 414 C1 NAG C 1 1555 1555 1.49 LINK ND2 ASN A 436 C1 NAG B 1 1555 1555 1.46 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.41 LINK NE2 HIS A 65 CU CU A 603 1555 1555 1.89 LINK ND1 HIS A 67 CU A CU A 602 1555 1555 2.07 LINK ND1 HIS A 67 CU B CU A 602 1555 1555 1.94 LINK NE2 HIS A 110 CU A CU A 602 1555 1555 2.10 LINK NE2 HIS A 110 CU B CU A 602 1555 1555 2.01 LINK NE2 HIS A 112 CU A CU A 601 1555 1555 2.15 LINK NE2 HIS A 112 CU B CU A 601 1555 1555 2.02 LINK O VAL A 317 NA NA A 612 1555 1555 2.38 LINK ND1 HIS A 397 CU CU A 604 1555 1555 2.04 LINK NE2 HIS A 400 CU CU A 603 1555 1555 1.89 LINK NE2 HIS A 402 CU A CU A 601 1555 1555 2.06 LINK NE2 HIS A 402 CU B CU A 601 1555 1555 1.95 LINK NE2 HIS A 452 CU A CU A 601 1555 1555 2.15 LINK NE2 HIS A 452 CU B CU A 601 1555 1555 1.95 LINK SG CYS A 453 CU CU A 604 1555 1555 2.19 LINK NE2 HIS A 454 CU A CU A 602 1555 1555 2.09 LINK NE2 HIS A 454 CU B CU A 602 1555 1555 2.07 LINK ND1 HIS A 458 CU CU A 604 1555 1555 2.03 LINK CU A CU A 601 O1 OXY A 609 1555 1555 2.09 LINK CU A CU A 601 O2 OXY A 609 1555 1555 2.15 LINK CU B CU A 601 O1 OXY A 609 1555 1555 2.69 LINK CU B CU A 601 O2 OXY A 609 1555 1555 2.66 LINK CU B CU A 601 O HOH A 701 1555 1555 2.21 LINK CU A CU A 601 O HOH A 704 1555 1555 1.93 LINK CU B CU A 601 O HOH A 704 1555 1555 2.53 LINK CU A CU A 601 O HOH A 705 1555 1555 2.52 LINK CU A CU A 602 O1 OXY A 609 1555 1555 2.17 LINK CU B CU A 602 O1 OXY A 609 1555 1555 2.62 LINK CU A CU A 602 O HOH A 704 1555 1555 2.33 LINK CU A CU A 602 O HOH A 705 1555 1555 2.39 LINK CU CU A 603 O HOH A 705 1555 1555 1.97 LINK CU CU A 603 O HOH A1029 1555 1555 2.06 LINK NA NA A 612 O HOH A 939 1555 1555 2.26 LINK NA NA A 612 O HOH A1175 1555 1555 2.03 LINK NA NA A 612 O HOH A1177 1555 1555 2.60 LINK NA NA A 612 O HOH A1196 1555 1555 2.61 LINK NA NA A 612 O HOH A1215 1555 1555 2.64 CISPEP 1 GLY A 4 PRO A 5 0 6.67 CISPEP 2 PHE A 32 PRO A 33 0 -15.78 CISPEP 3 LEU A 370 PRO A 371 0 2.14 CISPEP 4 GLY A 395 PRO A 396 0 0.51 CRYST1 56.440 84.450 112.510 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 0.017718 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008888 0.00000