HEADER TRANSFERASE/BIOSYNTHETIC PROTEIN 07-JUL-21 7RC6 TITLE AERONAMIDE N-METHYLTRANSFERASE, AERE, BOUND TO MODIFIED PEPTIDE TITLE 2 SUBSTRATE, AERA-DL,34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLTRANSFERASE FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AERONAMIDE A PEPTIDE; COMPND 7 CHAIN: C; COMPND 8 SYNONYM: AERA-DL; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MICROVIRGULA AERODENITRIFICANS DSM 15089; SOURCE 3 ORGANISM_TAXID: 1122240; SOURCE 4 GENE: AERE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MICROVIRGULA AERODENITRIFICANS DSM 15089; SOURCE 10 ORGANISM_TAXID: 1122240; SOURCE 11 GENE: AERA; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SAM-DEPENDENT, PEPTIDE CYTOTOXIN, PROTEUSIN, BIOSYNTHETIC PROTEIN, KEYWDS 2 TRANSFERASE-BIOSYNTHETIC PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.P.COGAN,R.REYES,S.K.NAIR REVDAT 3 15-NOV-23 7RC6 1 REMARK REVDAT 2 18-OCT-23 7RC6 1 REMARK REVDAT 1 30-MAR-22 7RC6 0 JRNL AUTH D.P.COGAN,A.BHUSHAN,R.REYES,L.ZHU,J.PIEL,S.K.NAIR JRNL TITL STRUCTURE AND MECHANISM FOR ITERATIVE AMIDE N -METHYLATION JRNL TITL 2 IN THE BIOSYNTHESIS OF CHANNEL-FORMING PEPTIDE CYTOTOXINS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 78119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35316135 JRNL DOI 10.1073/PNAS.2116578119 REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 58722 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 3006 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 40.7800 - 4.7300 0.99 2828 161 0.1725 0.1895 REMARK 3 2 4.7300 - 3.7500 1.00 2666 195 0.1310 0.1667 REMARK 3 3 3.7500 - 3.2800 1.00 2728 127 0.1473 0.1639 REMARK 3 4 3.2800 - 2.9800 1.00 2694 141 0.1688 0.1908 REMARK 3 5 2.9800 - 2.7700 1.00 2654 145 0.1622 0.1940 REMARK 3 6 2.7700 - 2.6000 1.00 2683 99 0.1684 0.1598 REMARK 3 7 2.6000 - 2.4700 1.00 2693 140 0.1671 0.1966 REMARK 3 8 2.4700 - 2.3700 1.00 2633 129 0.1585 0.1891 REMARK 3 9 2.3700 - 2.2700 1.00 2638 162 0.1598 0.1682 REMARK 3 10 2.2700 - 2.2000 1.00 2650 152 0.1657 0.1779 REMARK 3 11 2.2000 - 2.1300 1.00 2578 170 0.1721 0.1948 REMARK 3 12 2.1300 - 2.0700 1.00 2637 129 0.1719 0.1758 REMARK 3 13 2.0700 - 2.0100 1.00 2668 128 0.1752 0.2121 REMARK 3 14 2.0100 - 1.9600 1.00 2601 154 0.1682 0.1965 REMARK 3 15 1.9600 - 1.9200 1.00 2628 141 0.1681 0.2115 REMARK 3 16 1.9200 - 1.8800 1.00 2616 145 0.1769 0.2267 REMARK 3 17 1.8800 - 1.8400 1.00 2614 139 0.1900 0.2057 REMARK 3 18 1.8400 - 1.8100 1.00 2610 144 0.2055 0.2084 REMARK 3 19 1.8100 - 1.7700 1.00 2620 142 0.2103 0.2740 REMARK 3 20 1.7700 - 1.7400 1.00 2660 133 0.2403 0.2986 REMARK 3 21 1.7400 - 1.7100 1.00 2617 130 0.2687 0.2875 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.05 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: NULL REMARK 4 REMARK 4 7RC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1000257991. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-18 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 : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58778 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.710 REMARK 200 RESOLUTION RANGE LOW (A) : 67.575 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 14.80 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.10 REMARK 200 R MERGE FOR SHELL (I) : 1.04700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 7RC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 0.1 M SODIUM CITRATE PH REMARK 280 4.0, 0.2 M SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.26600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.13300 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.13300 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.26600 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: 2190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL 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 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 A 650 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 885 LIES ON A SPECIAL POSITION. 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 ASP A 377 REMARK 465 PRO A 378 REMARK 465 LEU A 379 REMARK 465 PRO A 380 REMARK 465 GLY A 381 REMARK 465 ALA A 382 REMARK 465 GLY A 383 REMARK 465 THR A 384 REMARK 465 DAL C -11 REMARK 465 ALA C -10 REMARK 465 DAL C -9 REMARK 465 ALA C -8 REMARK 465 DVA C -7 REMARK 465 VAL C -6 REMARK 465 DAL C 5 REMARK 465 ALA C 6 REMARK 465 DSG C 7 REMARK 465 GLY C 8 REMARK 465 DTH C 9 REMARK 465 VAL C 10 REMARK 465 DTH C 11 REMARK 465 ALA C 12 REMARK 465 DSG C 13 REMARK 465 ALA C 14 REMARK 465 DVA C 15 REMARK 465 ALA C 16 REMARK 465 DSG C 17 REMARK 465 THR C 18 REMARK 465 DSG C 19 REMARK 465 ALA C 20 REMARK 465 DVA C 21 REMARK 465 ALA C 22 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 LYS A 83 CG CD CE NZ REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 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 NH2 ARG A 361 O HOH A 501 2.03 REMARK 500 OG SER A 152 O HOH A 502 2.05 REMARK 500 O HOH A 588 O HOH A 646 2.06 REMARK 500 O HOH A 514 O HOH A 681 2.07 REMARK 500 NH2 ARG A 347 O HOH A 503 2.09 REMARK 500 O HOH A 769 O HOH A 841 2.10 REMARK 500 O HOH A 526 O HOH A 716 2.10 REMARK 500 O HOH A 548 O HOH A 641 2.10 REMARK 500 O HOH A 1028 O HOH A 1041 2.11 REMARK 500 O HOH A 943 O HOH A 953 2.16 REMARK 500 O HOH A 921 O HOH A 983 2.16 REMARK 500 O HOH A 512 O HOH A 819 2.17 REMARK 500 O HOH A 579 O HOH A 989 2.17 REMARK 500 O HOH A 711 O HOH A 975 2.17 REMARK 500 O HOH A 525 O HOH A 530 2.18 REMARK 500 O HOH A 812 O HOH A 930 2.18 REMARK 500 O HOH A 607 O HOH A 848 2.18 REMARK 500 O HOH A 839 O HOH A 935 2.19 REMARK 500 O HOH A 651 O HOH A 824 2.19 REMARK 500 O HOH A 882 O HOH A 911 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 503 O HOH A 871 4565 2.17 REMARK 500 O HOH A 536 O HOH A 593 4465 2.19 REMARK 500 O HOH A 501 O HOH A 593 4465 2.19 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 DSG C 1 CG DSG C 1 ND2 0.156 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 DSG C 1 CB - CA - C ANGL. DEV. = -13.3 DEGREES REMARK 500 DSG C 1 N - CA - CB ANGL. DEV. = 11.7 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 ALA A 30 154.12 77.43 REMARK 500 ALA A 109 -124.66 -106.86 REMARK 500 PHE A 129 -168.95 -118.56 REMARK 500 DSG C 1 -1.86 64.95 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 130 GLY A 131 145.98 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 A1031 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1032 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1033 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A1034 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1035 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A1036 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A1038 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A1039 DISTANCE = 6.88 ANGSTROMS REMARK 525 HOH A1040 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1041 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A1042 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH C 205 DISTANCE = 6.23 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 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 231 OD1 REMARK 620 2 PRO A 232 O 92.6 REMARK 620 3 HOH A 760 O 160.7 93.4 REMARK 620 4 DSG C 1 OD1 76.6 163.7 100.8 REMARK 620 N 1 2 3 DBREF1 7RC6 A 1 384 UNP A0A329B7M1_9NEIS DBREF2 7RC6 A A0A329B7M1 1 384 DBREF 7RC6 C -11 22 PDB 7RC6 7RC6 -11 22 SEQRES 1 A 384 MET THR PRO PRO LEU ALA THR THR ILE ASP ARG LEU ARG SEQRES 2 A 384 ASP TYR LEU ASP ARG VAL GLY PHE GLN GLN ILE TYR LYS SEQRES 3 A 384 TYR ILE VAL ALA VAL ASN HIS TYR ALA VAL THR PRO ALA SEQRES 4 A 384 LEU ILE THR ARG ASN THR ALA ALA SER VAL HIS HIS PHE SEQRES 5 A 384 PHE ASP SER ARG LEU GLY GLY ARG ALA GLU PHE ALA LEU SEQRES 6 A 384 LEU GLN CYS LEU MET THR GLY ARG PRO ALA GLU HIS ALA SEQRES 7 A 384 ALA LEU PRO ASP LYS ASP ARG ALA LEU ALA ASP ALA LEU SEQRES 8 A 384 VAL THR ALA GLY LEU LEU ARG ALA SER PRO ASP GLY ARG SEQRES 9 A 384 GLU VAL SER GLY ALA ASP ARG GLN LEU ILE SER ALA PHE SEQRES 10 A 384 GLY VAL ASP LEU LEU ILE ASP ARG ARG ILE HIS PHE GLY SEQRES 11 A 384 GLY GLU VAL HIS GLU VAL TYR ILE GLY PRO ASP SER TYR SEQRES 12 A 384 TRP MET LEU TYR TYR ILE ASN ALA SER GLY ILE ALA ARG SEQRES 13 A 384 THR HIS ARG ALA VAL ASP LEU CYS THR GLY SER GLY ILE SEQRES 14 A 384 ALA ALA LEU TYR LEU SER LEU PHE THR ASP HIS VAL LEU SEQRES 15 A 384 ALA THR ASP ILE GLY ASP VAL PRO LEU ALA LEU VAL GLU SEQRES 16 A 384 ILE ASN ARG ARG LEU ASN ARG ARG ASP ALA GLY THR MET SEQRES 17 A 384 GLU ILE ARG ARG GLU ASN LEU ASN ASP THR LEU ASP GLY SEQRES 18 A 384 ARG GLU ARG PHE ASP LEU LEU THR CYS ASN PRO PRO PHE SEQRES 19 A 384 VAL ALA PHE PRO PRO GLY TYR SER GLY THR LEU TYR SER SEQRES 20 A 384 GLN GLY THR GLY VAL ASP GLY LEU GLY TYR MET ARG ASP SEQRES 21 A 384 ILE VAL GLY ARG LEU PRO GLU VAL LEU ASN PRO GLY GLY SEQRES 22 A 384 SER ALA TYR LEU VAL ALA ASP LEU CYS GLY ASP ALA HIS SEQRES 23 A 384 GLY PRO HIS PHE LEU GLY GLU LEU GLU SER MET VAL THR SEQRES 24 A 384 GLY HIS GLY MET ARG ILE GLU ALA PHE ILE ASP HIS VAL SEQRES 25 A 384 LEU PRO ALA SER ALA GLN VAL GLY PRO ILE SER ASP PHE SEQRES 26 A 384 LEU ARG HIS ALA ALA GLY LEU PRO ALA ASP THR ASP ILE SEQRES 27 A 384 ALA ALA ASP VAL GLN ALA PHE GLN ARG GLU THR LEU ARG SEQRES 28 A 384 ALA ASP TYR TYR TYR LEU THR THR ILE ARG LEU GLN THR SEQRES 29 A 384 ALA ALA GLN ASN PRO GLY LEU ARG MET LEU ARG ARG ASP SEQRES 30 A 384 PRO LEU PRO GLY ALA GLY THR SEQRES 1 C 34 DAL ALA DAL ALA DVA VAL DTH TYR DLE GLY DAL ALA DSG SEQRES 2 C 34 VAL DVA GLY DAL ALA DSG GLY DTH VAL DTH ALA DSG ALA SEQRES 3 C 34 DVA ALA DSG THR DSG ALA DVA ALA HET DTH C -5 7 HET DLE C -3 8 HET DAL C -1 5 HET DSG C 1 8 HET DVA C 3 7 HET NA A 401 1 HET SAH C 101 26 HETNAM DTH D-THREONINE HETNAM DLE D-LEUCINE HETNAM DAL D-ALANINE HETNAM DSG D-ASPARAGINE HETNAM DVA D-VALINE HETNAM NA SODIUM ION HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE FORMUL 2 DTH C4 H9 N O3 FORMUL 2 DLE C6 H13 N O2 FORMUL 2 DAL C3 H7 N O2 FORMUL 2 DSG C4 H8 N2 O3 FORMUL 2 DVA C5 H11 N O2 FORMUL 3 NA NA 1+ FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 HOH *547(H2 O) HELIX 1 AA1 THR A 2 VAL A 19 1 18 HELIX 2 AA2 GLY A 20 ALA A 30 1 11 HELIX 3 AA3 THR A 45 LEU A 57 1 13 HELIX 4 AA4 ARG A 60 GLU A 62 5 3 HELIX 5 AA5 PHE A 63 THR A 71 1 9 HELIX 6 AA6 ALA A 78 LEU A 80 5 3 HELIX 7 AA7 PRO A 81 ALA A 94 1 14 HELIX 8 AA8 ARG A 126 HIS A 128 5 3 HELIX 9 AA9 GLY A 139 TYR A 148 1 10 HELIX 10 AB1 ASN A 150 ILE A 154 5 5 HELIX 11 AB2 GLY A 168 LEU A 176 1 9 HELIX 12 AB3 GLY A 187 ASN A 201 1 15 HELIX 13 AB4 ASN A 214 GLY A 221 1 8 HELIX 14 AB5 LEU A 255 VAL A 268 1 14 HELIX 15 AB6 PRO A 288 GLU A 293 1 6 HELIX 16 AB7 LEU A 294 GLY A 302 1 9 HELIX 17 AB8 ALA A 315 GLY A 331 1 17 HELIX 18 AB9 ASP A 337 THR A 349 1 13 SHEET 1 AA1 3 ALA A 75 GLU A 76 0 SHEET 2 AA1 3 GLU A 105 GLY A 108 -1 O VAL A 106 N ALA A 75 SHEET 3 AA1 3 LEU A 97 ALA A 99 -1 N ARG A 98 O SER A 107 SHEET 1 AA2 2 ARG A 111 ALA A 116 0 SHEET 2 AA2 2 VAL A 119 ASP A 124 -1 O LEU A 121 N ILE A 114 SHEET 1 AA3 8 MET A 208 ARG A 212 0 SHEET 2 AA3 8 HIS A 180 ASP A 185 1 N ALA A 183 O GLU A 209 SHEET 3 AA3 8 ARG A 159 LEU A 163 1 N ASP A 162 O LEU A 182 SHEET 4 AA3 8 PHE A 225 CYS A 230 1 O ASP A 226 N ARG A 159 SHEET 5 AA3 8 LEU A 269 GLY A 283 1 O ASN A 270 N PHE A 225 SHEET 6 AA3 8 TYR A 354 GLN A 363 -1 O TYR A 356 N LEU A 281 SHEET 7 AA3 8 ARG A 304 PRO A 314 -1 N PHE A 308 O THR A 359 SHEET 8 AA3 8 GLY A 370 LEU A 374 1 O LEU A 374 N ALA A 307 LINK C DTH C -5 N TYR C -4 1555 1555 1.33 LINK C TYR C -4 N DLE C -3 1555 1555 1.33 LINK C DLE C -3 N GLY C -2 1555 1555 1.33 LINK C GLY C -2 N DAL C -1 1555 1555 1.33 LINK C DAL C -1 N ALA C 0 1555 1555 1.34 LINK C ALA C 0 N DSG C 1 1555 1555 1.37 LINK C DSG C 1 N VAL C 2 1555 1555 1.33 LINK ND2 DSG C 1 SD SAH C 101 1555 1555 1.66 LINK C VAL C 2 N DVA C 3 1555 1555 1.34 LINK C DVA C 3 N GLY C 4 1555 1555 1.33 LINK OD1 ASN A 231 NA NA A 401 1555 1555 2.54 LINK O PRO A 232 NA NA A 401 1555 1555 2.35 LINK NA NA A 401 O HOH A 760 1555 1555 2.52 LINK NA NA A 401 OD1 DSG C 1 1555 1555 2.08 CRYST1 78.029 78.029 153.399 90.00 90.00 120.00 P 32 2 1 6 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 0.012816 0.007399 0.000000 0.00000 SCALE2 0.000000 0.014798 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006519 0.00000