HEADER TRANSFERASE 13-JUL-16 5GM8 TITLE METHYLATION AT POSITION 32 OF TRNA CATALYZED BY TRMJ ALTERS OXIDATIVE TITLE 2 STRESS RESPONSE IN PSEUDOMONAS AERUIGINOSA COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (CYTIDINE/URIDINE-2'-O-)-METHYLTRANSFERASE TRMJ; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 1-167; COMPND 5 SYNONYM: TRNA (CYTIDINE(32)/URIDINE(32)-2'-O)-METHYLTRANSFERASE,TRNA COMPND 6 CM32/UM32 METHYLTRANSFERASE; COMPND 7 EC: 2.1.1.200; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 STRAIN: B136-33; SOURCE 5 GENE: TRMJ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS PSEUDOMONAS AERUGINOSA, TRNA METHYLTRANSFERASE, TRMJ, OXIDATIVE KEYWDS 2 STRESS, TRNA MODIFICATION, WOBBLE BASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.JAROENSUK,S.ATICHARTPONGKUL,Y.H.CHIONH,Y.H.WONG,C.W.LIEW,M.E.MCBEE, AUTHOR 2 N.THONGDEE,E.G.PRESTWICH,M.S.DEMOTT,S.MONGKOLSUK,P.C.DEDON,J.LESCAR, AUTHOR 3 M.FUANGTHONG REVDAT 3 08-NOV-23 5GM8 1 REMARK REVDAT 2 13-DEC-17 5GM8 1 JRNL REMARK SEQRES REVDAT 1 26-OCT-16 5GM8 0 JRNL AUTH J.JAROENSUK,S.ATICHARTPONGKUL,Y.H.CHIONH,Y.H.WONG,C.W.LIEW, JRNL AUTH 2 M.E.MCBEE,N.THONGDEE,E.G.PRESTWICH,M.S.DEMOTT,S.MONGKOLSUK, JRNL AUTH 3 P.C.DEDON,J.LESCAR,M.FUANGTHONG JRNL TITL METHYLATION AT POSITION 32 OF TRNA CATALYZED BY TRMJ ALTERS JRNL TITL 2 OXIDATIVE STRESS RESPONSE IN PSEUDOMONAS AERUGINOSA. JRNL REF NUCLEIC ACIDS RES. V. 44 10834 2016 JRNL REFN ESSN 1362-4962 JRNL PMID 27683218 JRNL DOI 10.1093/NAR/GKW870 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 34917 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1753 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.26 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.67 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2849 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2370 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2707 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE : 0.2450 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.98 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 142 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.95 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60180 REMARK 3 B22 (A**2) : -1.22130 REMARK 3 B33 (A**2) : 0.61940 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.59500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.280 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.280 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.197 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.276 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.198 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5404 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7362 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1854 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 133 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 799 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5404 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 712 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6337 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.91 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.88 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300001049. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : TOROIDAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34918 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 20.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.63500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4CND REMARK 200 REMARK 200 REMARK: SOLID HEXAGONAL CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, LITHIUM REMARK 280 SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K 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 33.30500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 LEU C -5 REMARK 465 TYR C -4 REMARK 465 PHE C -3 REMARK 465 LEU D -5 REMARK 465 TYR D -4 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 ARG A 85 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 O HOH B 630 O HOH B 659 1.23 REMARK 500 O HOH A 672 O HOH A 675 1.54 REMARK 500 O HOH B 667 O HOH B 686 1.57 REMARK 500 NH2 ARG C 49 O HOH C 601 1.75 REMARK 500 NH1 ARG C 82 O HOH C 602 1.79 REMARK 500 O HOH A 653 O HOH A 660 1.91 REMARK 500 OE1 GLU C 95 O HOH C 603 1.99 REMARK 500 O HOH A 649 O HOH A 666 2.06 REMARK 500 CG GLU D 67 NH1 ARG D 128 2.08 REMARK 500 O HOH C 660 O HOH C 664 2.11 REMARK 500 O PRO D 89 O HOH D 601 2.12 REMARK 500 OD1 ASP B 3 O HOH B 601 2.14 REMARK 500 OG1 THR C 65 OE2 GLU C 68 2.16 REMARK 500 O HOH B 620 O HOH B 665 2.17 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 OE1 GLN A 127 O ILE B 86 1655 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 PHE D 141 CA PHE D 141 C 0.162 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 82 N - CA - C ANGL. DEV. = -20.0 DEGREES REMARK 500 ARG A 84 N - CA - C ANGL. DEV. = 23.9 DEGREES REMARK 500 PRO B 42 C - N - CD ANGL. DEV. = 14.9 DEGREES REMARK 500 GLU B 68 CA - C - O ANGL. DEV. = 12.7 DEGREES REMARK 500 SER B 74 C - N - CA ANGL. DEV. = 19.0 DEGREES REMARK 500 SER B 74 C - N - CA ANGL. DEV. = 16.1 DEGREES REMARK 500 SER B 74 N - CA - C ANGL. DEV. = 22.1 DEGREES REMARK 500 SER B 74 CA - C - O ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP B 83 CB - CA - C ANGL. DEV. = -20.6 DEGREES REMARK 500 ARG B 85 N - CA - C ANGL. DEV. = 19.5 DEGREES REMARK 500 TRP B 88 CB - CA - C ANGL. DEV. = -27.6 DEGREES REMARK 500 TRP B 88 N - CA - C ANGL. DEV. = 49.7 DEGREES REMARK 500 PRO B 89 C - N - CA ANGL. DEV. = 12.6 DEGREES REMARK 500 PRO B 89 C - N - CD ANGL. DEV. = -25.0 DEGREES REMARK 500 LEU B 90 N - CA - C ANGL. DEV. = 21.0 DEGREES REMARK 500 ASP C 83 CB - CA - C ANGL. DEV. = -14.2 DEGREES REMARK 500 LEU C 101 CA - CB - CG ANGL. DEV. = -15.4 DEGREES REMARK 500 PHE D 141 CA - C - O ANGL. DEV. = 13.4 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 -1 -8.31 -147.63 REMARK 500 SER A 31 -27.14 -140.56 REMARK 500 ALA A 50 47.81 -87.48 REMARK 500 ASP A 83 -156.62 -122.06 REMARK 500 ASN A 107 37.77 73.45 REMARK 500 PHE A 141 63.04 -158.03 REMARK 500 TYR B -4 -44.18 -133.67 REMARK 500 ALA B 50 44.36 -88.42 REMARK 500 PRO B 89 123.04 -33.49 REMARK 500 PHE B 141 -156.76 -105.11 REMARK 500 SER C 31 -42.52 -134.64 REMARK 500 ALA C 50 48.40 -83.17 REMARK 500 ALA C 81 -69.76 -96.06 REMARK 500 ASN C 107 32.78 71.47 REMARK 500 PHE C 141 68.27 -159.88 REMARK 500 PRO D 87 44.63 -89.07 REMARK 500 PHE D 141 74.17 -150.21 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 CYS B 73 SER B 74 149.94 REMARK 500 TRP B 88 PRO B 89 -135.74 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 676 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 677 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH B 690 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH C 674 DISTANCE = 7.88 ANGSTROMS REMARK 525 HOH D 648 DISTANCE = 7.93 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SFG D 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GMB RELATED DB: PDB REMARK 900 RELATED ID: 5GMC RELATED DB: PDB DBREF1 5GM8 A 1 167 UNP A0A072ZPM2_PSEAI DBREF2 5GM8 A A0A072ZPM2 1 167 DBREF1 5GM8 B 1 167 UNP A0A072ZPM2_PSEAI DBREF2 5GM8 B A0A072ZPM2 1 167 DBREF1 5GM8 C 1 167 UNP A0A072ZPM2_PSEAI DBREF2 5GM8 C A0A072ZPM2 1 167 DBREF1 5GM8 D 1 167 UNP A0A072ZPM2_PSEAI DBREF2 5GM8 D A0A072ZPM2 1 167 SEQADV 5GM8 LEU A -5 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 TYR A -4 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 PHE A -3 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 GLN A -2 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 SER A -1 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 MET A 0 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 LEU B -5 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 TYR B -4 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 PHE B -3 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 GLN B -2 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 SER B -1 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 MET B 0 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 LEU C -5 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 TYR C -4 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 PHE C -3 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 GLN C -2 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 SER C -1 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 MET C 0 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 LEU D -5 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 TYR D -4 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 PHE D -3 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 GLN D -2 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 SER D -1 UNP A0A072ZPM EXPRESSION TAG SEQADV 5GM8 MET D 0 UNP A0A072ZPM EXPRESSION TAG SEQRES 1 A 173 LEU TYR PHE GLN SER MET MET LEU ASP ARG ILE ARG VAL SEQRES 2 A 173 VAL LEU VAL ASN THR SER HIS PRO GLY ASN ILE GLY GLY SEQRES 3 A 173 ALA ALA ARG ALA MET LYS ASN MET GLY LEU SER GLN LEU SEQRES 4 A 173 VAL LEU VAL GLN PRO GLU SER PHE PRO HIS GLY ASP ALA SEQRES 5 A 173 VAL ALA ARG ALA SER GLY ALA THR ASP ILE LEU ASP ALA SEQRES 6 A 173 ALA ARG VAL VAL ASP THR LEU GLU GLU ALA LEU SER GLY SEQRES 7 A 173 CYS SER VAL VAL LEU GLY THR SER ALA ARG ASP ARG ARG SEQRES 8 A 173 ILE PRO TRP PRO LEU LEU ASP PRO ARG GLU CYS ALA THR SEQRES 9 A 173 THR CYS LEU GLU HIS LEU GLU ALA ASN GLY GLU VAL ALA SEQRES 10 A 173 LEU VAL PHE GLY ARG GLU TYR ALA GLY LEU THR ASN GLU SEQRES 11 A 173 GLU LEU GLN ARG CYS GLN PHE HIS VAL HIS ILE PRO SER SEQRES 12 A 173 ASP PRO GLU PHE GLY SER LEU ASN LEU ALA ALA ALA VAL SEQRES 13 A 173 GLN VAL LEU THR TYR GLU VAL ARG MET ALA TRP LEU ALA SEQRES 14 A 173 ALA GLN GLY LYS SEQRES 1 B 173 LEU TYR PHE GLN SER MET MET LEU ASP ARG ILE ARG VAL SEQRES 2 B 173 VAL LEU VAL ASN THR SER HIS PRO GLY ASN ILE GLY GLY SEQRES 3 B 173 ALA ALA ARG ALA MET LYS ASN MET GLY LEU SER GLN LEU SEQRES 4 B 173 VAL LEU VAL GLN PRO GLU SER PHE PRO HIS GLY ASP ALA SEQRES 5 B 173 VAL ALA ARG ALA SER GLY ALA THR ASP ILE LEU ASP ALA SEQRES 6 B 173 ALA ARG VAL VAL ASP THR LEU GLU GLU ALA LEU SER GLY SEQRES 7 B 173 CYS SER VAL VAL LEU GLY THR SER ALA ARG ASP ARG ARG SEQRES 8 B 173 ILE PRO TRP PRO LEU LEU ASP PRO ARG GLU CYS ALA THR SEQRES 9 B 173 THR CYS LEU GLU HIS LEU GLU ALA ASN GLY GLU VAL ALA SEQRES 10 B 173 LEU VAL PHE GLY ARG GLU TYR ALA GLY LEU THR ASN GLU SEQRES 11 B 173 GLU LEU GLN ARG CYS GLN PHE HIS VAL HIS ILE PRO SER SEQRES 12 B 173 ASP PRO GLU PHE GLY SER LEU ASN LEU ALA ALA ALA VAL SEQRES 13 B 173 GLN VAL LEU THR TYR GLU VAL ARG MET ALA TRP LEU ALA SEQRES 14 B 173 ALA GLN GLY LYS SEQRES 1 C 173 LEU TYR PHE GLN SER MET MET LEU ASP ARG ILE ARG VAL SEQRES 2 C 173 VAL LEU VAL ASN THR SER HIS PRO GLY ASN ILE GLY GLY SEQRES 3 C 173 ALA ALA ARG ALA MET LYS ASN MET GLY LEU SER GLN LEU SEQRES 4 C 173 VAL LEU VAL GLN PRO GLU SER PHE PRO HIS GLY ASP ALA SEQRES 5 C 173 VAL ALA ARG ALA SER GLY ALA THR ASP ILE LEU ASP ALA SEQRES 6 C 173 ALA ARG VAL VAL ASP THR LEU GLU GLU ALA LEU SER GLY SEQRES 7 C 173 CYS SER VAL VAL LEU GLY THR SER ALA ARG ASP ARG ARG SEQRES 8 C 173 ILE PRO TRP PRO LEU LEU ASP PRO ARG GLU CYS ALA THR SEQRES 9 C 173 THR CYS LEU GLU HIS LEU GLU ALA ASN GLY GLU VAL ALA SEQRES 10 C 173 LEU VAL PHE GLY ARG GLU TYR ALA GLY LEU THR ASN GLU SEQRES 11 C 173 GLU LEU GLN ARG CYS GLN PHE HIS VAL HIS ILE PRO SER SEQRES 12 C 173 ASP PRO GLU PHE GLY SER LEU ASN LEU ALA ALA ALA VAL SEQRES 13 C 173 GLN VAL LEU THR TYR GLU VAL ARG MET ALA TRP LEU ALA SEQRES 14 C 173 ALA GLN GLY LYS SEQRES 1 D 173 LEU TYR PHE GLN SER MET MET LEU ASP ARG ILE ARG VAL SEQRES 2 D 173 VAL LEU VAL ASN THR SER HIS PRO GLY ASN ILE GLY GLY SEQRES 3 D 173 ALA ALA ARG ALA MET LYS ASN MET GLY LEU SER GLN LEU SEQRES 4 D 173 VAL LEU VAL GLN PRO GLU SER PHE PRO HIS GLY ASP ALA SEQRES 5 D 173 VAL ALA ARG ALA SER GLY ALA THR ASP ILE LEU ASP ALA SEQRES 6 D 173 ALA ARG VAL VAL ASP THR LEU GLU GLU ALA LEU SER GLY SEQRES 7 D 173 CYS SER VAL VAL LEU GLY THR SER ALA ARG ASP ARG ARG SEQRES 8 D 173 ILE PRO TRP PRO LEU LEU ASP PRO ARG GLU CYS ALA THR SEQRES 9 D 173 THR CYS LEU GLU HIS LEU GLU ALA ASN GLY GLU VAL ALA SEQRES 10 D 173 LEU VAL PHE GLY ARG GLU TYR ALA GLY LEU THR ASN GLU SEQRES 11 D 173 GLU LEU GLN ARG CYS GLN PHE HIS VAL HIS ILE PRO SER SEQRES 12 D 173 ASP PRO GLU PHE GLY SER LEU ASN LEU ALA ALA ALA VAL SEQRES 13 D 173 GLN VAL LEU THR TYR GLU VAL ARG MET ALA TRP LEU ALA SEQRES 14 D 173 ALA GLN GLY LYS HET SFG A 500 27 HET SFG B 500 27 HET SFG C 500 27 HET SFG D 500 27 HETNAM SFG SINEFUNGIN HETSYN SFG ADENOSYL-ORNITHINE FORMUL 5 SFG 4(C15 H23 N7 O5) FORMUL 9 HOH *289(H2 O) HELIX 1 AA1 MET A 1 ASP A 3 5 3 HELIX 2 AA2 HIS A 14 MET A 28 1 15 HELIX 3 AA3 HIS A 43 ALA A 50 1 8 HELIX 4 AA4 ALA A 53 ALA A 60 1 8 HELIX 5 AA5 THR A 65 SER A 71 1 7 HELIX 6 AA6 ASP A 92 ALA A 106 1 15 HELIX 7 AA7 THR A 122 GLN A 127 1 6 HELIX 8 AA8 ASN A 145 ALA A 164 1 20 HELIX 9 AA9 GLN B -2 ASP B 3 5 6 HELIX 10 AB1 HIS B 14 GLY B 29 1 16 HELIX 11 AB2 HIS B 43 ALA B 50 1 8 HELIX 12 AB3 ALA B 53 ALA B 60 1 8 HELIX 13 AB4 THR B 65 SER B 71 1 7 HELIX 14 AB5 ASP B 92 LEU B 104 1 13 HELIX 15 AB6 GLU B 105 GLY B 108 5 4 HELIX 16 AB7 THR B 122 GLN B 127 1 6 HELIX 17 AB8 ASN B 145 GLN B 165 1 21 HELIX 18 AB9 GLN C -2 ASP C 3 5 6 HELIX 19 AC1 HIS C 14 MET C 28 1 15 HELIX 20 AC2 HIS C 43 ALA C 50 1 8 HELIX 21 AC3 ALA C 53 ALA C 60 1 8 HELIX 22 AC4 THR C 65 SER C 71 1 7 HELIX 23 AC5 ASP C 92 ALA C 106 1 15 HELIX 24 AC6 THR C 122 GLN C 127 1 6 HELIX 25 AC7 ASP C 138 GLY C 142 5 5 HELIX 26 AC8 ASN C 145 GLN C 165 1 21 HELIX 27 AC9 GLN D -2 ASP D 3 5 6 HELIX 28 AD1 HIS D 14 MET D 28 1 15 HELIX 29 AD2 HIS D 43 SER D 51 1 9 HELIX 30 AD3 ALA D 53 ALA D 60 1 8 HELIX 31 AD4 THR D 65 SER D 71 1 7 HELIX 32 AD5 ASP D 92 LEU D 104 1 13 HELIX 33 AD6 GLU D 105 GLY D 108 5 4 HELIX 34 AD7 THR D 122 ARG D 128 1 7 HELIX 35 AD8 ASN D 145 GLN D 165 1 21 SHEET 1 AA1 7 ARG A 61 VAL A 63 0 SHEET 2 AA1 7 GLN A 32 VAL A 36 1 N LEU A 35 O ARG A 61 SHEET 3 AA1 7 ILE A 5 VAL A 10 1 N VAL A 7 O VAL A 34 SHEET 4 AA1 7 VAL A 110 PHE A 114 1 O LEU A 112 N ARG A 6 SHEET 5 AA1 7 VAL A 75 THR A 79 1 N LEU A 77 O VAL A 113 SHEET 6 AA1 7 PHE A 131 VAL A 133 1 O VAL A 133 N GLY A 78 SHEET 7 AA1 7 LEU A 90 LEU A 91 1 N LEU A 91 O HIS A 132 SHEET 1 AA2 6 ARG B 61 VAL B 63 0 SHEET 2 AA2 6 GLN B 32 VAL B 36 1 N LEU B 35 O ARG B 61 SHEET 3 AA2 6 ILE B 5 VAL B 10 1 N LEU B 9 O VAL B 36 SHEET 4 AA2 6 VAL B 110 PHE B 114 1 O VAL B 110 N ARG B 6 SHEET 5 AA2 6 VAL B 75 THR B 79 1 N LEU B 77 O VAL B 113 SHEET 6 AA2 6 PHE B 131 VAL B 133 1 O VAL B 133 N GLY B 78 SHEET 1 AA3 7 ARG C 61 VAL C 63 0 SHEET 2 AA3 7 LEU C 33 VAL C 36 1 N LEU C 35 O ARG C 61 SHEET 3 AA3 7 ILE C 5 VAL C 10 1 N VAL C 7 O VAL C 34 SHEET 4 AA3 7 VAL C 110 PHE C 114 1 O LEU C 112 N VAL C 8 SHEET 5 AA3 7 VAL C 75 THR C 79 1 N LEU C 77 O VAL C 113 SHEET 6 AA3 7 PHE C 131 VAL C 133 1 O VAL C 133 N GLY C 78 SHEET 7 AA3 7 LEU C 90 LEU C 91 1 N LEU C 91 O HIS C 132 SHEET 1 AA4 7 ARG D 61 VAL D 63 0 SHEET 2 AA4 7 GLN D 32 VAL D 36 1 N LEU D 35 O ARG D 61 SHEET 3 AA4 7 ILE D 5 VAL D 10 1 N VAL D 7 O GLN D 32 SHEET 4 AA4 7 VAL D 110 PHE D 114 1 O LEU D 112 N VAL D 8 SHEET 5 AA4 7 VAL D 75 THR D 79 1 N LEU D 77 O VAL D 113 SHEET 6 AA4 7 PHE D 131 VAL D 133 1 O VAL D 133 N GLY D 78 SHEET 7 AA4 7 LEU D 90 LEU D 91 1 N LEU D 91 O HIS D 132 CISPEP 1 PHE A 41 PRO A 42 0 -1.73 CISPEP 2 ILE A 86 PRO A 87 0 1.37 CISPEP 3 PHE B 41 PRO B 42 0 1.46 CISPEP 4 PHE C 41 PRO C 42 0 2.54 CISPEP 5 PHE D 41 PRO D 42 0 -4.08 SITE 1 AC1 18 THR A 79 SER A 80 ALA A 81 ARG A 82 SITE 2 AC1 18 PHE A 114 GLY A 115 ARG A 116 GLU A 117 SITE 3 AC1 18 GLY A 120 VAL A 133 HIS A 134 ILE A 135 SITE 4 AC1 18 GLY A 142 SER A 143 LEU A 144 ALA A 149 SITE 5 AC1 18 HOH A 601 HOH A 605 SITE 1 AC2 20 THR B 79 SER B 80 ALA B 81 ARG B 82 SITE 2 AC2 20 PHE B 114 GLY B 115 ARG B 116 GLU B 117 SITE 3 AC2 20 TYR B 118 GLY B 120 VAL B 133 HIS B 134 SITE 4 AC2 20 ILE B 135 SER B 137 SER B 143 LEU B 144 SITE 5 AC2 20 ALA B 149 HOH B 604 HOH B 613 HOH B 618 SITE 1 AC3 20 THR C 79 SER C 80 ALA C 81 ARG C 82 SITE 2 AC3 20 PHE C 114 GLY C 115 ARG C 116 GLU C 117 SITE 3 AC3 20 TYR C 118 GLY C 120 VAL C 133 HIS C 134 SITE 4 AC3 20 ILE C 135 SER C 137 GLY C 142 SER C 143 SITE 5 AC3 20 LEU C 144 ALA C 149 HOH C 612 HOH C 614 SITE 1 AC4 18 THR D 79 SER D 80 ALA D 81 PHE D 114 SITE 2 AC4 18 GLY D 115 ARG D 116 GLU D 117 TYR D 118 SITE 3 AC4 18 GLY D 120 VAL D 133 HIS D 134 ILE D 135 SITE 4 AC4 18 SER D 137 GLY D 142 SER D 143 LEU D 144 SITE 5 AC4 18 ALA D 149 HOH D 617 CRYST1 56.520 66.610 98.580 90.00 101.96 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 0.017693 0.000000 0.003748 0.00000 SCALE2 0.000000 0.015013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010369 0.00000