HEADER VIRAL PROTEIN 18-FEB-20 6LZ8 TITLE CRYSTAL STRUCTURE OF MERS-COV N-NTD COMPLEXED WITH LIGAND P4-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPROTEIN; COMPND 3 CHAIN: A, C, B, D; COMPND 4 SYNONYM: NUCLEOCAPSID PROTEIN,PROTEIN N; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MIDDLE EAST RESPIRATORY SYNDROME-RELATED SOURCE 3 CORONAVIRUS; SOURCE 4 ORGANISM_TAXID: 1335626; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS, NUCLEOCAPSID PROTEIN, KEYWDS 2 N-TERMINAL DOMAIN, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.H.HOU,S.M.LIN,J.N.HSU REVDAT 3 29-NOV-23 6LZ8 1 REMARK REVDAT 2 07-SEP-22 6LZ8 1 JRNL REVDAT 1 24-FEB-21 6LZ8 0 JRNL AUTH J.N.HSU,J.S.CHEN,S.M.LIN,J.Y.HONG,Y.J.CHEN,U.S.JENG,S.Y.LUO, JRNL AUTH 2 M.H.HOU JRNL TITL TARGETING THE N-TERMINUS DOMAIN OF THE CORONAVIRUS JRNL TITL 2 NUCLEOCAPSID PROTEIN INDUCES ABNORMAL OLIGOMERIZATION VIA JRNL TITL 3 ALLOSTERIC MODULATION. JRNL REF FRONT MOL BIOSCI V. 9 71499 2022 JRNL REFN ESSN 2296-889X JRNL PMID 35517857 JRNL DOI 10.3389/FMOLB.2022.871499 REMARK 2 REMARK 2 RESOLUTION. 2.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.65 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.5 REMARK 3 NUMBER OF REFLECTIONS : 34259 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.560 REMARK 3 FREE R VALUE TEST SET COUNT : 3275 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 7.3177 - 5.8282 0.95 1568 170 0.2167 0.2776 REMARK 3 2 5.8282 - 5.0973 0.95 1573 162 0.2184 0.2454 REMARK 3 3 5.0973 - 4.6339 0.95 1603 167 0.2003 0.2160 REMARK 3 4 4.6339 - 4.3033 0.96 1628 176 0.2002 0.2496 REMARK 3 5 4.3033 - 4.0505 0.97 1637 171 0.2045 0.2514 REMARK 3 6 4.0505 - 3.8483 0.96 1583 167 0.2262 0.2556 REMARK 3 7 3.8483 - 3.6812 0.97 1655 180 0.2207 0.3260 REMARK 3 8 3.6812 - 3.5398 0.96 1542 166 0.2356 0.2974 REMARK 3 9 3.5398 - 3.4179 0.94 1601 172 0.2569 0.2998 REMARK 3 10 3.4179 - 3.3112 0.91 1543 160 0.2621 0.2787 REMARK 3 11 3.3112 - 3.2168 0.89 1461 151 0.2499 0.3161 REMARK 3 12 3.2168 - 3.1322 0.86 1474 148 0.2500 0.3525 REMARK 3 13 3.1322 - 3.0559 0.81 1354 142 0.2587 0.3179 REMARK 3 14 3.0559 - 2.9865 0.76 1230 121 0.2644 0.3509 REMARK 3 15 2.9865 - 2.9230 0.70 1165 131 0.2967 0.3790 REMARK 3 16 2.9230 - 2.8646 0.68 1152 125 0.2752 0.3239 REMARK 3 17 2.8646 - 2.8106 0.65 1103 117 0.2922 0.3405 REMARK 3 18 2.8106 - 2.7605 0.60 995 102 0.3065 0.3242 REMARK 3 19 2.7605 - 2.7138 0.58 941 104 0.2947 0.3503 REMARK 3 20 2.7138 - 2.6700 0.56 951 98 0.2957 0.4255 REMARK 3 21 2.6700 - 2.6290 0.54 902 98 0.2819 0.3660 REMARK 3 22 2.6290 - 2.5903 0.46 781 80 0.3002 0.3277 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.630 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.25 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I_MINUS AND I_PLUS COLUMNS. REMARK 4 REMARK 4 6LZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1300015751. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34259 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHENIX REMARK 200 STARTING MODEL: 4J3K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN 5 MG/ML, TRIS-HCL (PH=7.5) 25 REMARK 280 MM, NACL 75 MM, MES (PH=5.5) 140 MM ,(NH4)2SO4 75 MM, PEG 3350 REMARK 280 29 %, NABR 2 MM, LIGANDS 2 MM, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 55.51400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 ASN A 89 REMARK 465 THR A 165 REMARK 465 SER C 36 REMARK 465 HIS C 37 REMARK 465 MET C 38 REMARK 465 ASN C 39 REMARK 465 THR C 40 REMARK 465 GLN C 81 REMARK 465 ASP C 82 REMARK 465 ARG C 83 REMARK 465 LYS C 84 REMARK 465 ILE C 85 REMARK 465 ASN C 86 REMARK 465 THR C 87 REMARK 465 GLY C 88 REMARK 465 ASN C 89 REMARK 465 GLY C 90 REMARK 465 ILE C 91 REMARK 465 LYS C 92 REMARK 465 GLN C 93 REMARK 465 LEU C 94 REMARK 465 THR C 165 REMARK 465 SER D 36 REMARK 465 HIS D 37 REMARK 465 MET D 38 REMARK 465 ASN D 39 REMARK 465 ASP D 82 REMARK 465 ARG D 83 REMARK 465 LYS D 84 REMARK 465 ILE D 85 REMARK 465 ASN D 86 REMARK 465 THR D 87 REMARK 465 GLY D 88 REMARK 465 ASN D 89 REMARK 465 GLY D 90 REMARK 465 ILE D 91 REMARK 465 LYS D 92 REMARK 465 GLN D 93 REMARK 465 LEU D 94 REMARK 465 THR D 165 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 D 40 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 GLN B 73 O HOH B 201 1.82 REMARK 500 O HOH A 238 O HOH A 242 1.86 REMARK 500 NH1 ARG C 79 O HOH C 201 1.96 REMARK 500 O GLY A 88 O HOH A 201 2.02 REMARK 500 O HOH C 220 O HOH C 224 2.03 REMARK 500 O ASP A 82 O HOH A 202 2.04 REMARK 500 O PRO D 64 O HOH D 301 2.05 REMARK 500 O HOH A 246 O HOH A 247 2.06 REMARK 500 O HOH D 301 O HOH D 313 2.06 REMARK 500 OD1 ASN D 68 O HOH D 302 2.08 REMARK 500 OG SER A 133 O HOH A 203 2.08 REMARK 500 O GLY C 51 O HOH C 202 2.09 REMARK 500 O GLY D 136 O HOH D 303 2.09 REMARK 500 OE2 GLU C 125 O HOH C 203 2.11 REMARK 500 O THR C 129 O HOH C 204 2.14 REMARK 500 N THR A 87 O GLY A 90 2.15 REMARK 500 O HOH C 225 O HOH C 226 2.16 REMARK 500 NE2 GLN C 73 OG1 THR C 134 2.16 REMARK 500 NE2 GLN B 81 O HOH B 202 2.16 REMARK 500 OD1 ASN B 68 O HOH B 203 2.17 REMARK 500 O HOH A 226 O HOH A 236 2.18 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 NZ LYS A 155 OD2 ASP B 126 1455 1.67 REMARK 500 CE LYS A 155 OD2 ASP B 126 1455 2.09 REMARK 500 O ASN B 86 O HOH A 202 2555 2.11 REMARK 500 NZ LYS A 155 CB ASP B 126 1455 2.12 REMARK 500 ND2 ASN B 86 O HOH A 202 2555 2.13 REMARK 500 NZ LYS A 155 CG ASP B 126 1455 2.15 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 ARG D 114 CB ARG D 114 CG 0.217 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 LYS A 155 CD - CE - NZ ANGL. DEV. = -14.3 DEGREES REMARK 500 LYS C 52 CG - CD - CE ANGL. DEV. = -19.0 DEGREES REMARK 500 ARG B 83 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG D 114 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG D 114 NE - CZ - NH2 ANGL. DEV. = -8.2 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 ASP C 126 108.90 -54.81 REMARK 500 HIS B 124 136.36 -171.29 REMARK 500 SER D 69 -168.14 -101.46 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 ASN C 141 12.06 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 A 247 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH C 230 DISTANCE = 9.87 ANGSTROMS REMARK 525 HOH C 231 DISTANCE = 12.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EY9 D 201 DBREF1 6LZ8 A 39 165 UNP A0A2I2MQD0_9BETC DBREF2 6LZ8 A A0A2I2MQD0 39 165 DBREF1 6LZ8 C 39 165 UNP A0A2I2MQD0_9BETC DBREF2 6LZ8 C A0A2I2MQD0 39 165 DBREF1 6LZ8 B 39 165 UNP A0A2I2MQD0_9BETC DBREF2 6LZ8 B A0A2I2MQD0 39 165 DBREF1 6LZ8 D 39 165 UNP A0A2I2MQD0_9BETC DBREF2 6LZ8 D A0A2I2MQD0 39 165 SEQADV 6LZ8 SER A 36 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 HIS A 37 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 MET A 38 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 SER C 36 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 HIS C 37 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 MET C 38 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 SER B 36 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 HIS B 37 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 MET B 38 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 SER D 36 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 HIS D 37 UNP A0A2I2MQD EXPRESSION TAG SEQADV 6LZ8 MET D 38 UNP A0A2I2MQD EXPRESSION TAG SEQRES 1 A 130 SER HIS MET ASN THR VAL SER TRP TYR THR GLY LEU THR SEQRES 2 A 130 GLN HIS GLY LYS VAL PRO LEU THR PHE PRO PRO GLY GLN SEQRES 3 A 130 GLY VAL PRO LEU ASN ALA ASN SER THR PRO ALA GLN ASN SEQRES 4 A 130 ALA GLY TYR TRP ARG ARG GLN ASP ARG LYS ILE ASN THR SEQRES 5 A 130 GLY ASN GLY ILE LYS GLN LEU ALA PRO ARG TRP TYR PHE SEQRES 6 A 130 TYR TYR THR GLY THR GLY PRO GLU ALA ALA LEU PRO PHE SEQRES 7 A 130 ARG ALA VAL LYS ASP GLY ILE VAL TRP VAL HIS GLU ASP SEQRES 8 A 130 GLY ALA THR ASP ALA PRO SER THR PHE GLY THR ARG ASN SEQRES 9 A 130 PRO ASN ASN ASP SER ALA ILE VAL THR GLN PHE ALA PRO SEQRES 10 A 130 GLY THR LYS LEU PRO LYS ASN PHE HIS ILE GLU GLY THR SEQRES 1 C 130 SER HIS MET ASN THR VAL SER TRP TYR THR GLY LEU THR SEQRES 2 C 130 GLN HIS GLY LYS VAL PRO LEU THR PHE PRO PRO GLY GLN SEQRES 3 C 130 GLY VAL PRO LEU ASN ALA ASN SER THR PRO ALA GLN ASN SEQRES 4 C 130 ALA GLY TYR TRP ARG ARG GLN ASP ARG LYS ILE ASN THR SEQRES 5 C 130 GLY ASN GLY ILE LYS GLN LEU ALA PRO ARG TRP TYR PHE SEQRES 6 C 130 TYR TYR THR GLY THR GLY PRO GLU ALA ALA LEU PRO PHE SEQRES 7 C 130 ARG ALA VAL LYS ASP GLY ILE VAL TRP VAL HIS GLU ASP SEQRES 8 C 130 GLY ALA THR ASP ALA PRO SER THR PHE GLY THR ARG ASN SEQRES 9 C 130 PRO ASN ASN ASP SER ALA ILE VAL THR GLN PHE ALA PRO SEQRES 10 C 130 GLY THR LYS LEU PRO LYS ASN PHE HIS ILE GLU GLY THR SEQRES 1 B 130 SER HIS MET ASN THR VAL SER TRP TYR THR GLY LEU THR SEQRES 2 B 130 GLN HIS GLY LYS VAL PRO LEU THR PHE PRO PRO GLY GLN SEQRES 3 B 130 GLY VAL PRO LEU ASN ALA ASN SER THR PRO ALA GLN ASN SEQRES 4 B 130 ALA GLY TYR TRP ARG ARG GLN ASP ARG LYS ILE ASN THR SEQRES 5 B 130 GLY ASN GLY ILE LYS GLN LEU ALA PRO ARG TRP TYR PHE SEQRES 6 B 130 TYR TYR THR GLY THR GLY PRO GLU ALA ALA LEU PRO PHE SEQRES 7 B 130 ARG ALA VAL LYS ASP GLY ILE VAL TRP VAL HIS GLU ASP SEQRES 8 B 130 GLY ALA THR ASP ALA PRO SER THR PHE GLY THR ARG ASN SEQRES 9 B 130 PRO ASN ASN ASP SER ALA ILE VAL THR GLN PHE ALA PRO SEQRES 10 B 130 GLY THR LYS LEU PRO LYS ASN PHE HIS ILE GLU GLY THR SEQRES 1 D 130 SER HIS MET ASN THR VAL SER TRP TYR THR GLY LEU THR SEQRES 2 D 130 GLN HIS GLY LYS VAL PRO LEU THR PHE PRO PRO GLY GLN SEQRES 3 D 130 GLY VAL PRO LEU ASN ALA ASN SER THR PRO ALA GLN ASN SEQRES 4 D 130 ALA GLY TYR TRP ARG ARG GLN ASP ARG LYS ILE ASN THR SEQRES 5 D 130 GLY ASN GLY ILE LYS GLN LEU ALA PRO ARG TRP TYR PHE SEQRES 6 D 130 TYR TYR THR GLY THR GLY PRO GLU ALA ALA LEU PRO PHE SEQRES 7 D 130 ARG ALA VAL LYS ASP GLY ILE VAL TRP VAL HIS GLU ASP SEQRES 8 D 130 GLY ALA THR ASP ALA PRO SER THR PHE GLY THR ARG ASN SEQRES 9 D 130 PRO ASN ASN ASP SER ALA ILE VAL THR GLN PHE ALA PRO SEQRES 10 D 130 GLY THR LYS LEU PRO LYS ASN PHE HIS ILE GLU GLY THR HET EY9 D 201 14 HETNAM EY9 5-(2-METHOXYETHOXY)-1H-INDOLE FORMUL 5 EY9 C11 H13 N O2 FORMUL 6 HOH *124(H2 O) HELIX 1 AA1 THR A 70 GLN A 73 5 4 HELIX 2 AA2 THR A 105 ALA A 109 5 5 HELIX 3 AA3 THR C 70 GLN C 73 5 4 HELIX 4 AA4 THR C 105 ALA C 109 5 5 HELIX 5 AA5 THR B 70 GLN B 73 5 4 HELIX 6 AA6 THR B 105 ALA B 109 5 5 HELIX 7 AA7 THR D 70 GLN D 73 5 4 HELIX 8 AA8 THR D 105 ALA D 109 5 5 SHEET 1 AA1 5 ILE A 120 HIS A 124 0 SHEET 2 AA1 5 ALA A 75 GLN A 81 -1 N GLY A 76 O VAL A 123 SHEET 3 AA1 5 ARG A 97 TYR A 102 -1 O ARG A 97 N GLN A 81 SHEET 4 AA1 5 LEU A 47 THR A 48 -1 N LEU A 47 O TRP A 98 SHEET 5 AA1 5 HIS A 161 ILE A 162 -1 O HIS A 161 N THR A 48 SHEET 1 AA2 2 LYS A 84 ASN A 86 0 SHEET 2 AA2 2 ILE A 91 GLN A 93 -1 O LYS A 92 N ILE A 85 SHEET 1 AA3 5 ILE C 120 HIS C 124 0 SHEET 2 AA3 5 ALA C 75 ARG C 79 -1 N GLY C 76 O VAL C 123 SHEET 3 AA3 5 ARG C 97 TYR C 102 -1 O TYR C 99 N ARG C 79 SHEET 4 AA3 5 LEU C 47 GLN C 49 -1 N LEU C 47 O TRP C 98 SHEET 5 AA3 5 PHE C 160 ILE C 162 -1 O HIS C 161 N THR C 48 SHEET 1 AA4 5 ILE B 120 HIS B 124 0 SHEET 2 AA4 5 ALA B 75 GLN B 81 -1 N TRP B 78 O VAL B 121 SHEET 3 AA4 5 ARG B 97 TYR B 102 -1 O TYR B 99 N ARG B 79 SHEET 4 AA4 5 LEU B 47 THR B 48 -1 N LEU B 47 O TRP B 98 SHEET 5 AA4 5 HIS B 161 ILE B 162 -1 O HIS B 161 N THR B 48 SHEET 1 AA5 2 LYS B 84 ASN B 86 0 SHEET 2 AA5 2 ILE B 91 GLN B 93 -1 O LYS B 92 N ILE B 85 SHEET 1 AA6 5 ILE D 120 HIS D 124 0 SHEET 2 AA6 5 ALA D 75 ARG D 80 -1 N TRP D 78 O VAL D 121 SHEET 3 AA6 5 ARG D 97 TYR D 102 -1 O TYR D 101 N TYR D 77 SHEET 4 AA6 5 LEU D 47 GLN D 49 -1 N LEU D 47 O TRP D 98 SHEET 5 AA6 5 PHE D 160 ILE D 162 -1 O HIS D 161 N THR D 48 SITE 1 AC1 7 ASN B 141 ASN B 142 THR D 105 GLY D 136 SITE 2 AC1 7 THR D 137 LYS D 158 HIS D 161 CRYST1 35.154 111.028 92.261 90.00 100.97 90.00 P 1 21 1 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 0.028446 0.000000 0.005513 0.00000 SCALE2 0.000000 0.009007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011040 0.00000