HEADER OXIDOREDUCTASE 03-JUL-15 5A7E TITLE CRYSTALLOGRAPHIC STRUCTURAL DETERMINATION OF A TRIGONAL LACCASE FROM TITLE 2 CORIOLOPSIS GALLICA (CGL) TO 1.5 A RESOLUTION CAVEAT 5A7E BMA B 3 HAS WRONG CHIRALITY AT ATOM C2 BMA B 3 HAS WRONG CAVEAT 2 5A7E CHIRALITY AT ATOM C4 BMA C 3 HAS WRONG CHIRALITY AT ATOM C2 CAVEAT 3 5A7E MAN C 4 HAS WRONG CHIRALITY AT ATOM C1 MAN C 4 HAS WRONG CAVEAT 4 5A7E CHIRALITY AT ATOM C2 MAN C 5 HAS WRONG CHIRALITY AT ATOM C1 CAVEAT 5 5A7E MAN C 5 HAS WRONG CHIRALITY AT ATOM C2 BGC D 2 HAS WRONG CAVEAT 6 5A7E CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CORIOLOPSIS GALLICA LACCASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 22-517 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORIOLOPSIS GALLICA; SOURCE 3 ORGANISM_TAXID: 76126; SOURCE 4 STRAIN: LAC1 KEYWDS OXIDOREDUCTASE, CATALYTIC DOMAIN, LACCASE, MODELS, MOLECULAR, KEYWDS 2 OXIDATION-REDUCTION, PROTEIN CONFORMATION EXPDTA X-RAY DIFFRACTION AUTHOR R.R.RUIZ-ARELLANO,A.DIAZ,M.AYALA,E.DE LA MORA,E.RUDINO-PINERA REVDAT 7 31-JAN-24 5A7E 1 REMARK REVDAT 6 18-JAN-23 5A7E 1 CAVEAT COMPND REMARK HET REVDAT 6 2 1 HETNAM HETSYN FORMUL LINK REVDAT 6 3 1 ATOM REVDAT 5 07-DEC-22 5A7E 1 REMARK REVDAT 4 28-APR-21 5A7E 1 CAVEAT COMPND REMARK LINK REVDAT 4 2 1 ATOM REVDAT 3 29-JUL-20 5A7E 1 CAVEAT COMPND REMARK HETNAM REVDAT 3 2 1 HETSYN HELIX SHEET LINK REVDAT 3 3 1 SITE ATOM REVDAT 2 13-DEC-17 5A7E 1 AUTHOR JRNL REVDAT 1 25-MAY-16 5A7E 0 JRNL AUTH E.DE LA MORA,N.MORALES,G.RODRIGUEZ-ALMAZAN, JRNL AUTH 2 R.R.RUIZ-ARELLANO,E.RUDINO-PINIRA JRNL TITL METAL SITE DELOCALIZATION OBSERVED IN A MODEL MULTICOPPER JRNL TITL 2 OXIDASE: AN INSIGHT INTO WATER RELEASE MECHANISM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 81678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4051 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 43.0997 - 4.6067 0.93 2634 128 0.1373 0.1735 REMARK 3 2 4.6067 - 3.6571 0.97 2763 136 0.1189 0.1477 REMARK 3 3 3.6571 - 3.1950 0.97 2757 141 0.1418 0.1473 REMARK 3 4 3.1950 - 2.9029 0.97 2757 144 0.1491 0.1547 REMARK 3 5 2.9029 - 2.6949 0.97 2720 143 0.1645 0.1783 REMARK 3 6 2.6949 - 2.5360 0.96 2740 124 0.1679 0.1985 REMARK 3 7 2.5360 - 2.4090 0.97 2739 164 0.1700 0.1949 REMARK 3 8 2.4090 - 2.3042 0.96 2759 147 0.1646 0.1940 REMARK 3 9 2.3042 - 2.2155 0.96 2696 140 0.1702 0.1774 REMARK 3 10 2.2155 - 2.1390 0.96 2742 144 0.1705 0.1872 REMARK 3 11 2.1390 - 2.0721 0.95 2689 123 0.1820 0.1920 REMARK 3 12 2.0721 - 2.0129 0.95 2720 142 0.1773 0.1894 REMARK 3 13 2.0129 - 1.9599 0.95 2714 116 0.1730 0.1884 REMARK 3 14 1.9599 - 1.9121 0.94 2652 122 0.1832 0.2196 REMARK 3 15 1.9121 - 1.8686 0.93 2650 155 0.1809 0.1743 REMARK 3 16 1.8686 - 1.8289 0.94 2642 154 0.1882 0.2015 REMARK 3 17 1.8289 - 1.7923 0.95 2700 150 0.1854 0.2278 REMARK 3 18 1.7923 - 1.7585 0.93 2600 126 0.1856 0.1769 REMARK 3 19 1.7585 - 1.7271 0.94 2679 161 0.1839 0.1968 REMARK 3 20 1.7271 - 1.6978 0.94 2662 128 0.1919 0.2012 REMARK 3 21 1.6978 - 1.6704 0.93 2675 144 0.1931 0.2294 REMARK 3 22 1.6704 - 1.6447 0.94 2624 136 0.1944 0.2307 REMARK 3 23 1.6447 - 1.6205 0.92 2630 143 0.2041 0.2175 REMARK 3 24 1.6205 - 1.5977 0.93 2621 133 0.2001 0.2190 REMARK 3 25 1.5977 - 1.5761 0.92 2575 147 0.2066 0.2173 REMARK 3 26 1.5761 - 1.5556 0.93 2644 146 0.2038 0.2352 REMARK 3 27 1.5556 - 1.5362 0.92 2620 147 0.2217 0.2079 REMARK 3 28 1.5362 - 1.5177 0.92 2557 138 0.2205 0.2540 REMARK 3 29 1.5177 - 1.5000 0.91 2666 129 0.2265 0.2332 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) : 17.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.04 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09730 REMARK 3 B22 (A**2) : -0.02420 REMARK 3 B33 (A**2) : 0.12150 REMARK 3 B12 (A**2) : 0.80350 REMARK 3 B13 (A**2) : 0.86440 REMARK 3 B23 (A**2) : 1.00000 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 : 0.029 4198 REMARK 3 ANGLE : 2.025 5809 REMARK 3 CHIRALITY : 0.158 672 REMARK 3 PLANARITY : 0.013 775 REMARK 3 DIHEDRAL : 12.597 1429 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 5A7E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1290064268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.180760 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81678 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 43.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.970 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 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 2A2G REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17 M AMMONIUM SULPHATE, 25.5% PEG REMARK 280 8000, 15% GLYCEROL, PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 GLU A 307 CG CD OE1 OE2 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 C2 BMA C 3 O HOH A 1178 1.09 REMARK 500 O2 BMA C 3 O HOH A 1178 1.52 REMARK 500 CB ALA A 361 O HOH A 620 1.58 REMARK 500 O THR A 178 O HOH A 601 1.72 REMARK 500 N LEU A 179 O HOH A 602 1.73 REMARK 500 C THR A 178 O HOH A 602 1.77 REMARK 500 O3 BMA B 3 O HOH A 1176 1.83 REMARK 500 O HOH A 996 O HOH A 1041 1.84 REMARK 500 O HOH A 608 O HOH A 715 1.85 REMARK 500 O HOH A 1050 O HOH A 1163 1.86 REMARK 500 O HOH A 978 O HOH A 1012 1.86 REMARK 500 OD1 ASP A 41 O HOH A 603 1.86 REMARK 500 O HOH A 686 O HOH A 1050 1.88 REMARK 500 OG SER A 491 O HOH A 604 1.92 REMARK 500 O HOH A 990 O HOH A 1056 1.94 REMARK 500 O ASP A 377 O HOH A 605 1.94 REMARK 500 O3 BMA C 3 C4 MAN C 4 2.11 REMARK 500 O HOH A 889 O HOH A 1112 2.14 REMARK 500 O HOH A 924 O HOH A 1129 2.14 REMARK 500 N LEU A 322 O HOH A 605 2.15 REMARK 500 ND2 ASN A 432 O5 NAG C 1 2.16 REMARK 500 O THR A 178 N ALA A 180 2.16 REMARK 500 O THR A 178 N ALA A 180 2.16 REMARK 500 O HOH A 759 O HOH A 1001 2.17 REMARK 500 O6 BMA C 3 C2 MAN C 5 2.18 REMARK 500 O HOH A 1107 O HOH A 1119 2.18 REMARK 500 O HOH A 875 O HOH A 1095 2.19 REMARK 500 O HOH A 1034 O HOH A 1139 2.19 REMARK 500 O HOH A 1007 O HOH A 1024 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 603 O HOH A 691 1655 2.00 REMARK 500 O HOH A 1140 O HOH A 1154 1455 2.02 REMARK 500 O HOH A 1086 O HOH A 1171 1655 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 GLY A 121 C GLY A 121 O -0.101 REMARK 500 GLN A 266 CD GLN A 266 OE1 -0.184 REMARK 500 GLN A 266 CD GLN A 266 OE1 -0.184 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 130 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 THR A 178 N - CA - CB ANGL. DEV. = -12.1 DEGREES REMARK 500 ASN A 375 CA - C - N ANGL. DEV. = -19.2 DEGREES REMARK 500 ASN A 375 O - C - N ANGL. DEV. = 17.4 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 SER A 15 57.74 -145.89 REMARK 500 SER A 15 57.97 -144.21 REMARK 500 LEU A 57 124.69 79.03 REMARK 500 SER A 112 -137.58 50.73 REMARK 500 THR A 178 -36.68 -131.88 REMARK 500 LEU A 179 -20.05 33.70 REMARK 500 LEU A 179 -20.05 33.70 REMARK 500 ASP A 204 -69.66 -159.73 REMARK 500 ASP A 204 -69.66 -159.73 REMARK 500 ASP A 204 -69.66 -157.82 REMARK 500 ALA A 239 -4.35 79.33 REMARK 500 ASP A 253 -173.97 -174.15 REMARK 500 GLN A 266 60.18 -107.64 REMARK 500 GLN A 266 59.70 -107.28 REMARK 500 PRO A 315 60.08 -69.90 REMARK 500 LEU A 382 39.82 -143.86 REMARK 500 ASN A 417 53.68 -154.07 REMARK 500 PRO A 429 125.42 -39.36 REMARK 500 ASN A 474 70.30 -119.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A 176 -14.38 REMARK 500 SER A 176 13.45 REMARK 500 HIS A 400 -11.76 REMARK 500 HIS A 400 -10.13 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 A1169 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A1170 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A1175 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A1179 DISTANCE = 8.91 ANGSTROMS REMARK 525 HOH A1181 DISTANCE = 9.73 ANGSTROMS 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 BGC D 1 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 502 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HIS A 396 NE2 168.5 REMARK 620 3 HOH A 879 O 94.5 97.0 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 65 ND1 REMARK 620 2 HIS A 108 NE2 136.3 REMARK 620 3 HIS A 450 NE2 113.2 109.3 REMARK 620 N 1 2 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 110 NE2 REMARK 620 2 HIS A 398 NE2 118.9 REMARK 620 3 HIS A 448 NE2 117.4 120.8 REMARK 620 N 1 2 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 393 ND1 REMARK 620 2 CYS A 449 SG 125.3 REMARK 620 3 HIS A 454 ND1 101.3 132.3 REMARK 620 N 1 2 DBREF 5A7E A 0 495 UNP Q1W6B1 Q1W6B1_9APHY 22 517 SEQADV 5A7E ASP A 17 UNP Q1W6B1 TYR 39 CONFLICT SEQADV 5A7E ASN A 129 UNP Q1W6B1 GLN 151 CONFLICT SEQADV 5A7E LYS A 156 UNP Q1W6B1 ARG 178 CONFLICT SEQADV 5A7E ALA A 159 UNP Q1W6B1 PRO 181 CONFLICT SEQADV 5A7E PRO A 160 UNP Q1W6B1 ALA 182 CONFLICT SEQADV 5A7E VAL A 161 UNP Q1W6B1 ILE 183 CONFLICT SEQADV 5A7E SER A 176 UNP Q1W6B1 ILE 198 CONFLICT SEQADV 5A7E SER A 177 UNP Q1W6B1 ASN 199 CONFLICT SEQADV 5A7E ALA A 180 UNP Q1W6B1 ASN 202 CONFLICT SEQADV 5A7E TYR A 207 UNP Q1W6B1 HIS 229 CONFLICT SEQADV 5A7E LEU A 234 UNP Q1W6B1 ILE 256 CONFLICT SEQADV 5A7E THR A 265 UNP Q1W6B1 ASN 287 CONFLICT SEQADV 5A7E GLN A 266 UNP Q1W6B1 THR 288 CONFLICT SEQADV 5A7E ALA A 269 UNP Q1W6B1 ASP 291 CONFLICT SEQADV 5A7E THR A 272 UNP Q1W6B1 VAL 294 CONFLICT SEQADV 5A7E THR A 292 UNP Q1W6B1 ALA 314 CONFLICT SEQADV 5A7E ASN A 334 UNP Q1W6B1 ARG 356 CONFLICT SEQADV 5A7E THR A 336 UNP Q1W6B1 SER 358 CONFLICT SEQADV 5A7E ALA A 361 UNP Q1W6B1 GLN 383 CONFLICT SEQADV 5A7E ALA A 366 UNP Q1W6B1 THR 388 CONFLICT SEQADV 5A7E ALA A 386 UNP Q1W6B1 THR 408 CONFLICT SEQADV 5A7E ILE A 401 UNP Q1W6B1 ALA 423 CONFLICT SEQADV 5A7E ALA A 416 UNP Q1W6B1 GLU 438 CONFLICT SEQADV 5A7E ALA A 428 UNP Q1W6B1 SER 450 CONFLICT SEQRES 1 A 496 ALA ILE GLY PRO VAL ALA ASP LEU THR ILE SER ASN GLY SEQRES 2 A 496 ALA VAL SER PRO ASP GLY PHE SER ARG GLN ALA ILE LEU SEQRES 3 A 496 VAL ASN ASP VAL PHE PRO SER PRO LEU ILE THR GLY ASN SEQRES 4 A 496 LYS GLY ASP ARG PHE GLN LEU ASN VAL ILE ASP ASN MET SEQRES 5 A 496 THR ASN HIS THR MET LEU LYS SER THR SER ILE HIS TRP SEQRES 6 A 496 HIS GLY PHE PHE GLN HIS GLY THR ASN TRP ALA ASP GLY SEQRES 7 A 496 PRO ALA PHE VAL ASN GLN CYS PRO ILE SER THR GLY HIS SEQRES 8 A 496 ALA PHE LEU TYR ASP PHE GLN VAL PRO ASP GLN ALA GLY SEQRES 9 A 496 THR PHE TRP TYR HIS SER HIS LEU SER THR GLN TYR CYS SEQRES 10 A 496 ASP GLY LEU ARG GLY PRO ILE VAL VAL TYR ASP PRO ASN SEQRES 11 A 496 ASP PRO HIS LYS SER LEU TYR ASP VAL ASP ASP ASP SER SEQRES 12 A 496 THR VAL ILE THR LEU ALA ASP TRP TYR HIS LEU ALA ALA SEQRES 13 A 496 LYS VAL GLY ALA PRO VAL PRO THR ALA ASP ALA THR LEU SEQRES 14 A 496 ILE ASN GLY LEU GLY ARG SER SER SER THR LEU ALA ALA SEQRES 15 A 496 ASP LEU ALA VAL ILE THR VAL THR LYS GLY LYS ARG TYR SEQRES 16 A 496 ARG PHE ARG LEU VAL SER LEU SER CYS ASP PRO ASN TYR SEQRES 17 A 496 THR PHE SER ILE ASP GLY HIS SER LEU THR VAL ILE GLU SEQRES 18 A 496 ALA ASP SER VAL ASN LEU LYS PRO HIS THR VAL ASP SER SEQRES 19 A 496 LEU GLN ILE PHE ALA ALA GLN ARG TYR SER PHE VAL LEU SEQRES 20 A 496 ASN ALA ASP GLN ASP VAL ASP ASN TYR TRP ILE ARG ALA SEQRES 21 A 496 LEU PRO ASN SER GLY THR GLN ASN PHE ALA GLY GLY THR SEQRES 22 A 496 ASN SER ALA ILE LEU ARG TYR ASP GLY ALA ALA PRO VAL SEQRES 23 A 496 GLU PRO THR THR SER GLN THR PRO SER THR ASN PRO LEU SEQRES 24 A 496 VAL GLU SER ALA LEU THR THR LEU GLU GLY THR ALA ALA SEQRES 25 A 496 PRO GLY SER PRO THR PRO GLY GLY VAL ASP LEU ALA LEU SEQRES 26 A 496 ASN MET ALA PHE GLY PHE ALA GLY GLY ASN PHE THR ILE SEQRES 27 A 496 ASN GLY ALA SER PHE THR PRO PRO THR VAL PRO VAL LEU SEQRES 28 A 496 LEU GLN ILE LEU SER GLY ALA GLN SER ALA ALA ASP LEU SEQRES 29 A 496 LEU PRO ALA GLY SER VAL TYR SER LEU PRO ALA ASN ALA SEQRES 30 A 496 ASP ILE GLU ILE SER LEU PRO ALA THR ALA ALA ALA PRO SEQRES 31 A 496 GLY PHE PRO HIS PRO PHE HIS LEU HIS GLY HIS ILE PHE SEQRES 32 A 496 ALA VAL VAL ARG SER ALA GLY SER SER THR TYR ASN TYR SEQRES 33 A 496 ALA ASN PRO VAL TYR ARG ASP VAL VAL SER THR GLY ALA SEQRES 34 A 496 PRO GLY ASP ASN VAL THR ILE ARG PHE ARG THR ASP ASN SEQRES 35 A 496 PRO GLY PRO TRP PHE LEU HIS CYS HIS ILE ASP PHE HIS SEQRES 36 A 496 LEU GLU ALA GLY PHE ALA VAL VAL MET ALA GLU ASP ILE SEQRES 37 A 496 PRO ASP VAL ALA ALA THR ASN PRO VAL PRO GLN ALA TRP SEQRES 38 A 496 SER ASP LEU CYS PRO THR TYR ASP ALA LEU SER PRO ASP SEQRES 39 A 496 ASP GLN MODRES 5A7E ASN A 53 ASN GLYCOSYLATION SITE MODRES 5A7E ASN A 432 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET MAN C 5 11 HET BGC D 1 11 HET BGC D 2 11 HET CU A 501 1 HET CU A 502 1 HET CU A 503 1 HET CU A 504 1 HET ACT A 505 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM CU COPPER (II) ION HETNAM ACT ACETATE 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 HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 2 BMA 2(C6 H12 O6) FORMUL 3 MAN 2(C6 H12 O6) FORMUL 4 BGC 2(C6 H12 O6) FORMUL 5 CU 4(CU 2+) FORMUL 9 ACT C2 H3 O2 1- FORMUL 10 HOH *581(H2 O) HELIX 1 AA1 THR A 72 ASP A 76 5 5 HELIX 2 AA2 THR A 113 GLY A 118 5 6 HELIX 3 AA3 HIS A 132 TYR A 136 5 5 HELIX 4 AA4 ASP A 140 SER A 142 5 3 HELIX 5 AA5 PHE A 268 THR A 272 5 5 HELIX 6 AA6 VAL A 299 LEU A 303 5 5 HELIX 7 AA7 PRO A 348 SER A 355 1 8 HELIX 8 AA8 SER A 359 LEU A 363 5 5 HELIX 9 AA9 ILE A 451 ALA A 457 1 7 HELIX 10 AB1 ASP A 469 ASN A 474 1 6 HELIX 11 AB2 PRO A 477 ASP A 482 1 6 HELIX 12 AB3 ASP A 482 ALA A 489 1 8 HELIX 13 AB4 SER A 491 GLN A 495 5 5 SHEET 1 AA1 4 ARG A 21 VAL A 26 0 SHEET 2 AA1 4 VAL A 4 VAL A 14 -1 N SER A 10 O LEU A 25 SHEET 3 AA1 4 ARG A 42 ASP A 49 1 O ASN A 46 N LEU A 7 SHEET 4 AA1 4 ALA A 91 GLN A 97 -1 O PHE A 96 N PHE A 43 SHEET 1 AA2 4 ILE A 35 ASN A 38 0 SHEET 2 AA2 4 ARG A 120 TYR A 126 1 O TYR A 126 N GLY A 37 SHEET 3 AA2 4 GLY A 103 SER A 109 -1 N PHE A 105 O ILE A 123 SHEET 4 AA2 4 ILE A 62 HIS A 65 -1 N HIS A 63 O HIS A 108 SHEET 1 AA3 6 ALA A 166 ILE A 169 0 SHEET 2 AA3 6 VAL A 144 TRP A 150 -1 N ALA A 148 O LEU A 168 SHEET 3 AA3 6 ARG A 193 SER A 200 1 O ARG A 197 N ILE A 145 SHEET 4 AA3 6 ARG A 241 ASN A 247 -1 O TYR A 242 N LEU A 198 SHEET 5 AA3 6 LEU A 216 ALA A 221 -1 N THR A 217 O VAL A 245 SHEET 6 AA3 6 VAL A 224 VAL A 231 -1 O VAL A 231 N LEU A 216 SHEET 1 AA4 5 VAL A 185 VAL A 188 0 SHEET 2 AA4 5 SER A 274 TYR A 279 1 O ILE A 276 N ILE A 186 SHEET 3 AA4 5 ASN A 254 PRO A 261 -1 N TYR A 255 O LEU A 277 SHEET 4 AA4 5 TYR A 207 ILE A 211 -1 N SER A 210 O ARG A 258 SHEET 5 AA4 5 LEU A 234 ILE A 236 -1 O LEU A 234 N PHE A 209 SHEET 1 AA5 5 LEU A 322 ASN A 325 0 SHEET 2 AA5 5 ASP A 377 PRO A 383 1 O GLU A 379 N LEU A 324 SHEET 3 AA5 5 ASN A 432 ARG A 438 -1 O PHE A 437 N ILE A 378 SHEET 4 AA5 5 PHE A 402 ARG A 406 -1 N ALA A 403 O ARG A 436 SHEET 5 AA5 5 TYR A 420 ARG A 421 -1 O ARG A 421 N PHE A 402 SHEET 1 AA6 2 PHE A 328 ALA A 331 0 SHEET 2 AA6 2 ASN A 334 ILE A 337 -1 O THR A 336 N GLY A 329 SHEET 1 AA7 5 VAL A 369 LEU A 372 0 SHEET 2 AA7 5 ALA A 460 GLU A 465 1 O VAL A 462 N TYR A 370 SHEET 3 AA7 5 GLY A 443 CYS A 449 -1 N TRP A 445 O MET A 463 SHEET 4 AA7 5 PRO A 394 LEU A 397 -1 N HIS A 396 O HIS A 448 SHEET 5 AA7 5 VAL A 423 SER A 425 -1 O VAL A 424 N PHE A 395 SSBOND 1 CYS A 116 CYS A 203 1555 1555 2.13 LINK ND2 ASN A 53 C1 NAG B 1 1555 1555 1.43 LINK ND2 ASN A 432 C1 NAG C 1 1555 1555 1.39 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.20 LINK O4 NAG B 2 C4 BMA B 3 1555 1555 1.24 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.41 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.31 LINK O3 BMA C 3 C3 MAN C 4 1555 1555 1.01 LINK O6 BMA C 3 C1 MAN C 5 1555 1555 1.26 LINK O2 BGC D 1 C1 BGC D 2 1555 1555 1.16 LINK NE2 HIS A 63 CU CU A 502 1555 1555 1.93 LINK ND1 HIS A 65 CU CU A 501 1555 1555 1.96 LINK NE2 HIS A 108 CU CU A 501 1555 1555 2.13 LINK NE2 HIS A 110 CU CU A 504 1555 1555 2.07 LINK ND1 HIS A 393 CU CU A 503 1555 1555 2.11 LINK NE2 HIS A 396 CU CU A 502 1555 1555 1.92 LINK NE2 HIS A 398 CU CU A 504 1555 1555 2.03 LINK NE2 HIS A 448 CU CU A 504 1555 1555 2.02 LINK SG CYS A 449 CU CU A 503 1555 1555 2.18 LINK NE2 HIS A 450 CU CU A 501 1555 1555 2.16 LINK ND1 HIS A 454 CU CU A 503 1555 1555 2.11 LINK CU CU A 502 O HOH A 879 1555 1555 2.66 CISPEP 1 GLY A 2 PRO A 3 0 5.53 CISPEP 2 PHE A 30 PRO A 31 0 -0.67 CISPEP 3 LEU A 364 PRO A 365 0 2.57 CISPEP 4 PHE A 391 PRO A 392 0 3.80 CRYST1 45.742 56.406 59.173 75.67 73.03 76.49 P 1 1 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 0.021862 -0.005253 -0.005767 0.00000 SCALE2 0.000000 0.018233 -0.003583 0.00000 SCALE3 0.000000 0.000000 0.018007 0.00000