HEADER OXIDOREDUCTASE 25-APR-16 5G3C TITLE PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 CASE TITLE 2 IN THERMUS TERMOPHILUS MULTICOPPER OXIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMUS THERMOPHILUS MULTICOPPER OXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.10.3.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 274 KEYWDS OXIDOREDUCTASE, MULTICOPPER OXIDASE, RADIATION DAMAGE, METALLIC KEYWDS 2 SITES, MACROMOLECULAR CRYSTALLOGRAPHY, RADICAL SCAVENGERS EXPDTA X-RAY DIFFRACTION AUTHOR R.RUIZ-ARELLANO,A.DIAZ,E.ROSAS,E.RUDINO REVDAT 2 10-JAN-24 5G3C 1 REMARK LINK REVDAT 1 07-JUN-17 5G3C 0 JRNL AUTH R.RUIZ-ARELLANO,A.DIAZ,E.ROSAS,V.STOJANOFF,E.RUDINO JRNL TITL PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE JRNL TITL 2 CUT2 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49653 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.6609 - 4.5681 0.94 2662 122 0.1460 0.1600 REMARK 3 2 4.5681 - 3.6333 0.97 2636 129 0.1118 0.1190 REMARK 3 3 3.6333 - 3.1762 0.98 2654 140 0.1220 0.1388 REMARK 3 4 3.1762 - 2.8868 0.99 2641 145 0.1242 0.1484 REMARK 3 5 2.8868 - 2.6805 0.99 2627 137 0.1327 0.1651 REMARK 3 6 2.6805 - 2.5228 0.99 2654 132 0.1378 0.1825 REMARK 3 7 2.5228 - 2.3967 0.99 2623 146 0.1371 0.1606 REMARK 3 8 2.3967 - 2.2925 1.00 2630 152 0.1316 0.1660 REMARK 3 9 2.2925 - 2.2044 0.99 2636 135 0.1314 0.1568 REMARK 3 10 2.2044 - 2.1284 0.99 2605 135 0.1403 0.1875 REMARK 3 11 2.1284 - 2.0619 0.99 2636 128 0.1394 0.1803 REMARK 3 12 2.0619 - 2.0030 0.99 2590 147 0.1609 0.2097 REMARK 3 13 2.0030 - 1.9503 0.99 2600 141 0.1496 0.1796 REMARK 3 14 1.9503 - 1.9028 0.99 2614 127 0.1495 0.2249 REMARK 3 15 1.9028 - 1.8596 0.99 2601 128 0.1511 0.2016 REMARK 3 16 1.8596 - 1.8200 0.99 2596 149 0.1488 0.2058 REMARK 3 17 1.8200 - 1.7836 0.99 2587 154 0.1494 0.1918 REMARK 3 18 1.7836 - 1.7500 0.98 2597 117 0.1581 0.1987 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 4049 REMARK 3 ANGLE : 1.668 5576 REMARK 3 CHIRALITY : 0.129 605 REMARK 3 PLANARITY : 0.011 740 REMARK 3 DIHEDRAL : 16.211 1578 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5G3C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-16. REMARK 100 THE DEPOSITION ID IS D_1290066728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 393350 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 19.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 17.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 2YAE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.24200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.24200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.87200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.16600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.87200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.16600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 48.24200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.87200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 55.16600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 48.24200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.87200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 55.16600 REMARK 290 SMTRY3 8 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: 6990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.4 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -93.74400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.24200 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2157 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2335 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2340 LIES ON A SPECIAL POSITION. 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 THR A 338 O HOH A 2425 1.88 REMARK 500 NH1 ARG A 430 O HOH A 2485 1.97 REMARK 500 O HOH A 2066 O HOH A 2116 2.07 REMARK 500 O HOH A 2244 O HOH A 2480 2.07 REMARK 500 NE2 GLN A 56 O HOH A 2078 2.09 REMARK 500 O HOH A 2080 O HOH A 2272 2.11 REMARK 500 O HOH A 2353 O HOH A 2355 2.12 REMARK 500 O HOH A 2138 O HOH A 2294 2.14 REMARK 500 O HOH A 2424 O HOH A 2500 2.15 REMARK 500 NZ LYS A 374 O HOH A 2477 2.15 REMARK 500 NZ LYS A 43 O HOH A 2062 2.16 REMARK 500 O HOH A 2068 O HOH A 2142 2.17 REMARK 500 O HOH A 2091 O HOH A 2279 2.17 REMARK 500 O HOH A 2096 O HOH A 2187 2.18 REMARK 500 O HOH A 2075 O HOH A 2143 2.18 REMARK 500 NE2 GLN A 56 O HOH A 2078 2.18 REMARK 500 O HOH A 2042 O HOH A 2055 2.19 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 O HOH A 2210 O HOH A 2526 8455 2.01 REMARK 500 NZ LYS A 331 O HOH A 2353 4565 2.10 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 GLU A 157 CB GLU A 157 CG -0.114 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 221 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 234 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 LYS A 424 CD - CE - NZ ANGL. DEV. = 14.0 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 ARG A 77 -1.41 76.82 REMARK 500 ARG A 77 -2.15 77.99 REMARK 500 HIS A 137 56.08 -146.21 REMARK 500 ALA A 230 -20.27 -151.29 REMARK 500 ALA A 247 -155.88 -99.09 REMARK 500 MET A 301 -172.47 65.63 REMARK 500 ASN A 323 64.05 39.28 REMARK 500 LEU A 333 -99.43 -117.35 REMARK 500 LEU A 333 -100.38 -117.35 REMARK 500 VAL A 399 -35.83 73.01 REMARK 500 ARG A 436 -95.43 -107.84 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 GLY A 300 MET A 301 146.00 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 A2049 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH A2147 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A2539 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A2541 DISTANCE = 5.87 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 A1465 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 ND1 REMARK 620 2 HIS A 135 NE2 144.2 REMARK 620 3 HIS A 446 NE2 104.6 110.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1464 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 393 ND1 REMARK 620 2 CYS A 445 SG 122.2 REMARK 620 3 HIS A 450 ND1 106.3 131.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A1463 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 398 NE2 REMARK 620 2 HIS A 444 NE2 121.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1476 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2064 O REMARK 620 2 HOH A2069 O 98.0 REMARK 620 3 HOH A2538 O 107.5 125.1 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1463 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1464 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1466 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1467 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1468 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1471 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1472 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1473 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1474 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 1475 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1476 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 1477 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5G3B RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE: THE CUT2 REMARK 900 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE REMARK 900 RELATED ID: 5G3D RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 REMARK 900 CCASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE REMARK 900 RELATED ID: 5G3E RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 REMARK 900 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE REMARK 900 RELATED ID: 5G3F RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 REMARK 900 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE REMARK 900 RELATED ID: 5G3G RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 REMARK 900 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE REMARK 900 RELATED ID: 5G3H RELATED DB: PDB REMARK 900 PRESERVING METALLIC SITES AFFECTED BY RADIATION DAMAGE THE CUT2 REMARK 900 CASE IN THERMUS THERMOPHILUS MULTICOPPER OXIDASE DBREF 5G3C A 24 462 UNP I7AL37 I7AL37_THETH 24 462 SEQADV 5G3C ILE A 53 UNP I7AL37 LEU 53 CONFLICT SEQADV 5G3C THR A 123 UNP I7AL37 ALA 123 CONFLICT SEQRES 1 A 439 GLY PRO SER PHE PRO GLU PRO LYS VAL VAL ARG SER GLN SEQRES 2 A 439 GLY GLY LEU LEU SER LEU LYS LEU SER ALA THR PRO THR SEQRES 3 A 439 PRO LEU ALA ILE ALA GLY GLN ARG ALA THR LEU LEU THR SEQRES 4 A 439 TYR GLY GLY SER PHE PRO GLY PRO THR LEU ARG VAL ARG SEQRES 5 A 439 PRO ARG ASP THR VAL ARG LEU THR LEU GLU ASN ARG LEU SEQRES 6 A 439 PRO GLU PRO THR ASN LEU HIS TRP HIS GLY LEU PRO ILE SEQRES 7 A 439 SER PRO LYS VAL ASP ASP PRO PHE LEU GLU ILE PRO PRO SEQRES 8 A 439 GLY GLU SER TRP THR TYR GLU PHE THR VAL PRO LYS GLU SEQRES 9 A 439 LEU ALA GLY THR PHE TRP TYR HIS PRO HIS LEU HIS GLY SEQRES 10 A 439 ARG VAL ALA PRO GLN LEU PHE ALA GLY LEU LEU GLY ALA SEQRES 11 A 439 LEU VAL VAL GLU SER SER LEU ASP ALA ILE PRO GLU LEU SEQRES 12 A 439 ARG GLU ALA GLU GLU HIS LEU LEU VAL LEU LYS ASP LEU SEQRES 13 A 439 ALA LEU GLN GLY GLY ARG PRO ALA PRO HIS THR PRO MET SEQRES 14 A 439 ASP TRP MET ASN GLY LYS GLU GLY ASP LEU VAL LEU VAL SEQRES 15 A 439 ASN GLY ALA LEU ARG PRO THR LEU VAL ALA GLN LYS ALA SEQRES 16 A 439 THR LEU ARG LEU ARG LEU LEU ASN ALA SER ASN ALA ARG SEQRES 17 A 439 TYR TYR ARG LEU ALA LEU GLN ASP HIS PRO LEU TYR LEU SEQRES 18 A 439 ILE ALA ALA ASP GLY GLY PHE LEU GLU GLU PRO LEU GLU SEQRES 19 A 439 VAL SER GLU LEU LEU LEU ALA PRO GLY GLU ARG ALA GLU SEQRES 20 A 439 VAL LEU VAL ARG LEU ARG LYS GLU GLY ARG PHE LEU LEU SEQRES 21 A 439 GLN ALA LEU PRO TYR ASP ARG GLY ALA MET GLY MET MET SEQRES 22 A 439 ASP MET GLY GLY MET ALA HIS ALA MET PRO GLN GLY PRO SEQRES 23 A 439 SER ARG PRO GLU THR LEU LEU TYR LEU ILE ALA PRO LYS SEQRES 24 A 439 ASN PRO LYS PRO LEU PRO LEU PRO LYS ALA LEU SER PRO SEQRES 25 A 439 PHE PRO THR LEU PRO ALA PRO VAL VAL THR ARG ARG LEU SEQRES 26 A 439 VAL LEU THR GLU ASP MET MET ALA ALA ARG PHE PHE ILE SEQRES 27 A 439 ASN GLY GLN VAL PHE ASP HIS ARG ARG VAL ASP LEU LYS SEQRES 28 A 439 GLY GLN ALA GLN THR VAL GLU VAL TRP GLU VAL GLU ASN SEQRES 29 A 439 GLN GLY ASP MET ASP HIS PRO PHE HIS LEU HIS VAL HIS SEQRES 30 A 439 PRO PHE GLN VAL LEU SER VAL GLY GLY ARG PRO PHE PRO SEQRES 31 A 439 TYR ARG ALA TRP LYS ASP VAL VAL ASN LEU LYS ALA GLY SEQRES 32 A 439 GLU VAL ALA ARG LEU LEU VAL PRO LEU ARG GLU LYS GLY SEQRES 33 A 439 ARG THR VAL PHE HIS CYS HIS ILE VAL GLU HIS GLU ASP SEQRES 34 A 439 ARG GLY MET MET GLY VAL LEU GLU VAL GLY HET CU A1463 1 HET CU A1464 1 HET CU A1465 1 HET MPD A1466 8 HET MPD A1467 8 HET MRD A1468 8 HET MPD A1469 8 HET MRD A1470 8 HET MPD A1471 8 HET MPD A1472 8 HET MPD A1473 8 HET MRD A1474 8 HET MRD A1475 8 HET NA A1476 1 HET MPD A1477 8 HETNAM CU COPPER (II) ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETNAM NA SODIUM ION FORMUL 2 CU 3(CU 2+) FORMUL 5 MPD 7(C6 H14 O2) FORMUL 7 MRD 4(C6 H14 O2) FORMUL 15 NA NA 1+ FORMUL 17 HOH *542(H2 O) HELIX 1 1 ARG A 141 ALA A 148 1 8 HELIX 2 2 SER A 158 ALA A 162 5 5 HELIX 3 3 ILE A 163 GLU A 168 1 6 HELIX 4 4 THR A 190 GLY A 197 1 8 HELIX 5 5 MET A 354 ALA A 357 5 4 HELIX 6 6 ILE A 447 ARG A 453 1 7 SHEET 1 AA 5 VAL A 32 ARG A 34 0 SHEET 2 AA 5 THR A 71 VAL A 74 1 O THR A 71 N VAL A 33 SHEET 3 AA 5 GLY A 152 VAL A 156 1 O ALA A 153 N LEU A 72 SHEET 4 AA 5 GLY A 130 HIS A 135 -1 O GLY A 130 N VAL A 156 SHEET 5 AA 5 HIS A 95 HIS A 97 -1 O HIS A 95 N HIS A 135 SHEET 1 AB 4 GLN A 56 TYR A 63 0 SHEET 2 AB 4 LEU A 39 ILE A 53 -1 O THR A 47 N THR A 62 SHEET 3 AB 4 THR A 79 ASN A 86 1 O THR A 79 N LEU A 40 SHEET 4 AB 4 SER A 117 THR A 123 -1 O TRP A 118 N LEU A 84 SHEET 1 AC 7 ALA A 208 LEU A 209 0 SHEET 2 AC 7 LEU A 202 VAL A 205 -1 O VAL A 205 N ALA A 208 SHEET 3 AC 7 GLU A 170 LEU A 179 -1 O LYS A 177 N LEU A 204 SHEET 4 AC 7 THR A 219 ASN A 226 1 O THR A 219 N GLU A 170 SHEET 5 AC 7 ARG A 268 ARG A 274 -1 O ALA A 269 N LEU A 224 SHEET 6 AC 7 LEU A 242 ALA A 247 -1 O TYR A 243 N LEU A 272 SHEET 7 AC 7 GLY A 250 VAL A 258 -1 O GLY A 250 N ALA A 247 SHEET 1 AD 2 LEU A 181 GLN A 182 0 SHEET 2 AD 2 ARG A 185 PRO A 186 -1 O ARG A 185 N GLN A 182 SHEET 1 AE 5 THR A 212 VAL A 214 0 SHEET 2 AE 5 GLU A 313 ALA A 320 1 O TYR A 317 N LEU A 213 SHEET 3 AE 5 GLY A 279 LEU A 286 -1 O GLY A 279 N ALA A 320 SHEET 4 AE 5 TYR A 233 LEU A 237 -1 O ARG A 234 N LEU A 286 SHEET 5 AE 5 LEU A 261 LEU A 263 -1 O LEU A 261 N LEU A 235 SHEET 1 AF 2 MET A 293 MET A 296 0 SHEET 2 AF 2 HIS A 303 PRO A 306 -1 O HIS A 303 N MET A 296 SHEET 1 AG 6 ARG A 358 ILE A 361 0 SHEET 2 AG 6 VAL A 344 ASP A 353 -1 O THR A 351 N PHE A 360 SHEET 3 AG 6 VAL A 380 ASN A 387 1 O VAL A 382 N ARG A 346 SHEET 4 AG 6 VAL A 428 PRO A 434 -1 O ALA A 429 N VAL A 385 SHEET 5 AG 6 PHE A 402 VAL A 407 -1 O GLN A 403 N LEU A 432 SHEET 6 AG 6 ARG A 410 PRO A 411 1 O ARG A 410 N VAL A 407 SHEET 1 AH 6 ARG A 358 ILE A 361 0 SHEET 2 AH 6 VAL A 344 ASP A 353 -1 O THR A 351 N PHE A 360 SHEET 3 AH 6 VAL A 380 ASN A 387 1 O VAL A 382 N ARG A 346 SHEET 4 AH 6 VAL A 428 PRO A 434 -1 O ALA A 429 N VAL A 385 SHEET 5 AH 6 PHE A 402 VAL A 407 -1 O GLN A 403 N LEU A 432 SHEET 6 AH 6 TRP A 417 LYS A 418 -1 O LYS A 418 N PHE A 402 SHEET 1 AI 2 ARG A 410 PRO A 411 0 SHEET 2 AI 2 PHE A 402 VAL A 407 1 O VAL A 407 N ARG A 410 SHEET 1 AJ 5 LEU A 373 GLY A 375 0 SHEET 2 AJ 5 MET A 456 VAL A 461 1 O VAL A 458 N LEU A 373 SHEET 3 AJ 5 GLY A 439 CYS A 445 -1 O GLY A 439 N VAL A 461 SHEET 4 AJ 5 HIS A 393 LEU A 397 -1 O HIS A 396 N HIS A 444 SHEET 5 AJ 5 VAL A 420 LEU A 423 -1 O VAL A 421 N PHE A 395 LINK ND1 HIS A 97 CU CU A1465 1555 1555 1.98 LINK NE2 HIS A 135 CU CU A1465 1555 1555 2.00 LINK ND1 HIS A 393 CU CU A1464 1555 1555 2.08 LINK NE2 HIS A 398 CU CU A1463 1555 1555 1.74 LINK NE2 HIS A 444 CU CU A1463 1555 1555 1.78 LINK SG CYS A 445 CU CU A1464 1555 1555 2.15 LINK NE2 HIS A 446 CU CU A1465 1555 1555 2.11 LINK ND1 HIS A 450 CU CU A1464 1555 1555 2.17 LINK NA NA A1476 O HOH A2064 1555 1555 2.55 LINK NA NA A1476 O HOH A2069 1555 1555 2.64 LINK NA NA A1476 O HOH A2538 1555 1555 2.46 CISPEP 1 PHE A 67 PRO A 68 0 -10.70 CISPEP 2 MET A 301 ALA A 302 0 -8.42 SITE 1 AC1 3 HIS A 137 HIS A 398 HIS A 444 SITE 1 AC2 3 HIS A 393 CYS A 445 HIS A 450 SITE 1 AC3 5 HIS A 95 HIS A 97 TRP A 133 HIS A 135 SITE 2 AC3 5 HIS A 446 SITE 1 AC4 7 ASP A 248 LEU A 263 GLU A 267 ARG A 268 SITE 2 AC4 7 TYR A 414 LYS A 418 MRD A1470 SITE 1 AC5 5 ARG A 280 TYR A 317 HOH A2408 HOH A2534 SITE 2 AC5 5 HOH A2535 SITE 1 AC6 9 GLU A 127 LEU A 128 ALA A 129 SER A 158 SITE 2 AC6 9 SER A 334 HOH A2216 HOH A2217 HOH A2343 SITE 3 AC6 9 HOH A2422 SITE 1 AC7 3 GLU A 257 SER A 259 HOH A2339 SITE 1 AC8 7 LEU A 256 VAL A 258 GLU A 260 LEU A 261 SITE 2 AC8 7 PRO A 413 MPD A1466 HOH A2366 SITE 1 AC9 8 PRO A 25 SER A 26 VAL A 214 GLN A 216 SITE 2 AC9 8 ASN A 362 GLN A 364 HOH A2005 HOH A2461 SITE 1 BC1 2 PRO A 191 MPD A1473 SITE 1 BC2 6 GLY A 140 TRP A 194 ASP A 452 ARG A 453 SITE 2 BC2 6 MPD A1472 HOH A2235 SITE 1 BC3 3 LYS A 31 GLY A 64 HOH A2106 SITE 1 BC4 5 PRO A 337 LEU A 339 ARG A 436 HOH A2103 SITE 2 BC4 5 HOH A2537 SITE 1 BC5 4 THR A 47 HOH A2064 HOH A2069 HOH A2538 SITE 1 BC6 2 MET A 295 MET A 355 CRYST1 93.744 110.332 96.484 90.00 90.00 90.00 C 2 2 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 0.010667 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009064 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010364 0.00000