PDB Short entry for 2IYF HEADER TRANSFERASE 17-JUL-06 2IYF TITLE THE CRYSTAL STRUCTURE OF MACROLIDE GLYCOSYLTRANSFERASES: A TITLE 2 BLUEPRINT FOR ANTIBIOTIC ENGINEERING COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLEANDOMYCIN GLYCOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: OLED; COMPND 5 EC: 2.4.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES ANTIBIOTICUS; SOURCE 3 ORGANISM_TAXID: 1890; SOURCE 4 STRAIN: DSM 40868; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET32B KEYWDS ANTIBIOTIC RESISTANCE, GLYCOSYLATION, GLYCOSYLTRANSFERASE, KEYWDS 2 ENZYME, MACROLIDE, TRANSFERASE, CARBOHYDRATE EXPDTA X-RAY DIFFRACTION AUTHOR D.N.BOLAM,S.M.ROBERTS,M.R.PROCTOR,J.P.TURKENBURG,E.J.DODSON, AUTHOR 2 C.MARTINEZ-FLEITES,M.YANG,B.G.DAVIS,G.J.DAVIES,H.J.GILBERT REVDAT 5 07-AUG-13 2IYF 1 SOURCE REMARK VERSN DBREF REVDAT 5 2 SEQADV SEQRES REVDAT 4 24-FEB-09 2IYF 1 VERSN REVDAT 3 29-JAN-08 2IYF 1 JRNL REVDAT 2 10-APR-07 2IYF 1 JRNL REMARK REVDAT 1 27-MAR-07 2IYF 0 JRNL AUTH D.N.BOLAM,S.M.ROBERTS,M.R.PROCTOR,J.P.TURKENBURG, JRNL AUTH 2 E.J.DODSON,C.MARTINEZ-FLEITES,M.YANG,B.G.DAVIS, JRNL AUTH 3 G.J.DAVIES,H.J.GILBERT JRNL TITL THE CRYSTAL STRUCTURE OF TWO MACROLIDE JRNL TITL 2 GLYCOSYLTRANSFERASES PROVIDES A BLUEPRINT FOR HOST JRNL TITL 3 CELL ANTIBIOTIC IMMUNITY. JRNL REF PROC.NAT.ACAD.SCI.USA V. 104 5336 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17376874 JRNL DOI 10.1073/PNAS.0607897104 REMARK 2 REMARK 2 RESOLUTION. 1.7 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 89255 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4762 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6418 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2550 REMARK 3 BIN FREE R VALUE SET COUNT : 336 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5939 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 153 REMARK 3 SOLVENT ATOMS : 604 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.07000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.110 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.074 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.199 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6259 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8592 ; 1.513 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 786 ; 5.521 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;37.751 ;23.223 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 897 ;13.614 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 54 ;19.012 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 972 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4822 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2948 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4303 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 489 ; 0.187 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 45 ; 0.178 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.124 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3987 ; 0.888 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6250 ; 1.394 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2553 ; 2.154 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2334 ; 3.334 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2IYF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-06. REMARK 100 THE PDBE ID CODE IS EBI-29380. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 30.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.4 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.06 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.3 REMARK 200 R MERGE FOR SHELL (I) : 0.41 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.82 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-23% PEG8K,0.2M MGCL2,0.1M REMARK 280 TRIS-HCL PH 8.5 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 32.88900 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 MET A 0 REMARK 465 THR A 1 REMARK 465 THR A 2 REMARK 465 GLN A 3 REMARK 465 THR A 4 REMARK 465 THR A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 216 REMARK 465 ASP A 217 REMARK 465 ARG A 218 REMARK 465 ALA A 219 REMARK 465 GLU A 220 REMARK 465 LYS A 244 REMARK 465 ARG A 270 REMARK 465 LYS A 271 REMARK 465 VAL A 272 REMARK 465 ARG A 400 REMARK 465 HIS A 401 REMARK 465 GLU A 402 REMARK 465 ARG A 403 REMARK 465 GLN A 404 REMARK 465 GLU A 405 REMARK 465 PRO A 406 REMARK 465 VAL A 407 REMARK 465 GLY A 408 REMARK 465 ASP A 409 REMARK 465 ARG A 410 REMARK 465 PRO A 411 REMARK 465 ASN A 412 REMARK 465 GLY A 413 REMARK 465 GLY A 414 REMARK 465 MET B 0 REMARK 465 THR B 1 REMARK 465 THR B 2 REMARK 465 GLN B 3 REMARK 465 THR B 4 REMARK 465 ALA B 399 REMARK 465 ARG B 400 REMARK 465 HIS B 401 REMARK 465 GLU B 402 REMARK 465 ARG B 403 REMARK 465 GLN B 404 REMARK 465 GLU B 405 REMARK 465 PRO B 406 REMARK 465 VAL B 407 REMARK 465 GLY B 408 REMARK 465 ASP B 409 REMARK 465 ARG B 410 REMARK 465 PRO B 411 REMARK 465 ASN B 412 REMARK 465 GLY B 413 REMARK 465 GLY B 414 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 PRO A 54 CG CD REMARK 470 ARG A 159 NH1 NH2 REMARK 470 GLN A 215 CB CG CD OE1 NE2 REMARK 470 GLN A 225 CG CD OE1 NE2 REMARK 470 GLU A 231 CD OE1 OE2 REMARK 470 PHE A 242 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 276 CG CD OE1 OE2 REMARK 470 LEU A 277 CB CG CD1 CD2 REMARK 470 GLU A 279 CG CD OE1 OE2 REMARK 470 VAL A 328 CB CG1 CG2 REMARK 470 ARG A 344 CZ NH1 NH2 REMARK 470 GLU A 349 C CG CD OE1 OE2 REMARK 470 ASP A 354 CG OD1 OD2 REMARK 470 GLU A 368 CD OE1 OE2 REMARK 470 THR B 5 CG2 REMARK 470 PRO B 54 CG CD REMARK 470 ASP B 69 CB CG OD1 OD2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 LYS B 138 CD CE NZ REMARK 470 LYS B 170 CD CE NZ REMARK 470 GLU B 176 CD OE1 OE2 REMARK 470 ASP B 201 CG OD1 OD2 REMARK 470 GLU B 205 OE1 REMARK 470 GLU B 220 CB CG CD OE1 OE2 REMARK 470 GLN B 225 CG CD OE1 NE2 REMARK 470 GLU B 279 CG CD OE1 OE2 REMARK 470 ARG B 344 CZ NH1 NH2 REMARK 470 ARG B 357 CZ NH1 NH2 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 REMARK 500 MG MG B 1401 O HOH B 2164 1445 2.00 REMARK 500 O HOH B 2164 MG MG B 1401 1455 2.00 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 GLN B 90 N - CA - CB ANGL. DEV. = -11.8 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 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 VAL A 20 -50.38 -126.03 REMARK 500 ASP A 102 62.66 -156.95 REMARK 500 VAL A 144 -53.54 -122.49 REMARK 500 LEU A 191 30.24 -93.78 REMARK 500 PHE A 242 49.16 -87.77 REMARK 500 ASP A 329 0.32 -65.42 REMARK 500 ASP B 102 59.10 -152.66 REMARK 500 VAL B 144 -55.97 -123.12 REMARK 500 CYS B 214 77.22 -112.98 REMARK 500 ALA B 241 -51.27 -123.01 REMARK 500 VAL B 328 -124.45 44.77 REMARK 500 REMARK 500 REMARK: NULL 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 MG B1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B2216 O REMARK 620 2 THR B 317 O 85.2 REMARK 620 3 HOH B2213 O 88.3 89.6 REMARK 620 4 HOH B2212 O 172.6 91.9 84.9 REMARK 620 5 HOH B2215 O 96.2 92.7 175.1 90.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERY A1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP A1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ERY B1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UDP B1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B1401 DBREF 2IYF A 0 414 UNP Q3HTL6 Q3HTL6_STRAT 1 415 DBREF 2IYF B 0 414 UNP Q3HTL6 Q3HTL6_STRAT 1 415 SEQADV 2IYF PRO A 54 UNP Q3HTL6 ALA 55 CONFLICT SEQADV 2IYF PRO B 54 UNP Q3HTL6 ALA 55 CONFLICT SEQRES 1 A 415 MET THR THR GLN THR THR PRO ALA HIS ILE ALA MET PHE SEQRES 2 A 415 SER ILE ALA ALA HIS GLY HIS VAL ASN PRO SER LEU GLU SEQRES 3 A 415 VAL ILE ARG GLU LEU VAL ALA ARG GLY HIS ARG VAL THR SEQRES 4 A 415 TYR ALA ILE PRO PRO VAL PHE ALA ASP LYS VAL ALA ALA SEQRES 5 A 415 THR GLY PRO ARG PRO VAL LEU TYR HIS SER THR LEU PRO SEQRES 6 A 415 GLY PRO ASP ALA ASP PRO GLU ALA TRP GLY SER THR LEU SEQRES 7 A 415 LEU ASP ASN VAL GLU PRO PHE LEU ASN ASP ALA ILE GLN SEQRES 8 A 415 ALA LEU PRO GLN LEU ALA ASP ALA TYR ALA ASP ASP ILE SEQRES 9 A 415 PRO ASP LEU VAL LEU HIS ASP ILE THR SER TYR PRO ALA SEQRES 10 A 415 ARG VAL LEU ALA ARG ARG TRP GLY VAL PRO ALA VAL SER SEQRES 11 A 415 LEU SER PRO ASN LEU VAL ALA TRP LYS GLY TYR GLU GLU SEQRES 12 A 415 GLU VAL ALA GLU PRO MET TRP ARG GLU PRO ARG GLN THR SEQRES 13 A 415 GLU ARG GLY ARG ALA TYR TYR ALA ARG PHE GLU ALA TRP SEQRES 14 A 415 LEU LYS GLU ASN GLY ILE THR GLU HIS PRO ASP THR PHE SEQRES 15 A 415 ALA SER HIS PRO PRO ARG SER LEU VAL LEU ILE PRO LYS SEQRES 16 A 415 ALA LEU GLN PRO HIS ALA ASP ARG VAL ASP GLU ASP VAL SEQRES 17 A 415 TYR THR PHE VAL GLY ALA CYS GLN GLY ASP ARG ALA GLU SEQRES 18 A 415 GLU GLY GLY TRP GLN ARG PRO ALA GLY ALA GLU LYS VAL SEQRES 19 A 415 VAL LEU VAL SER LEU GLY SER ALA PHE THR LYS GLN PRO SEQRES 20 A 415 ALA PHE TYR ARG GLU CYS VAL ARG ALA PHE GLY ASN LEU SEQRES 21 A 415 PRO GLY TRP HIS LEU VAL LEU GLN ILE GLY ARG LYS VAL SEQRES 22 A 415 THR PRO ALA GLU LEU GLY GLU LEU PRO ASP ASN VAL GLU SEQRES 23 A 415 VAL HIS ASP TRP VAL PRO GLN LEU ALA ILE LEU ARG GLN SEQRES 24 A 415 ALA ASP LEU PHE VAL THR HIS ALA GLY ALA GLY GLY SER SEQRES 25 A 415 GLN GLU GLY LEU ALA THR ALA THR PRO MET ILE ALA VAL SEQRES 26 A 415 PRO GLN ALA VAL ASP GLN PHE GLY ASN ALA ASP MET LEU SEQRES 27 A 415 GLN GLY LEU GLY VAL ALA ARG LYS LEU ALA THR GLU GLU SEQRES 28 A 415 ALA THR ALA ASP LEU LEU ARG GLU THR ALA LEU ALA LEU SEQRES 29 A 415 VAL ASP ASP PRO GLU VAL ALA ARG ARG LEU ARG ARG ILE SEQRES 30 A 415 GLN ALA GLU MET ALA GLN GLU GLY GLY THR ARG ARG ALA SEQRES 31 A 415 ALA ASP LEU ILE GLU ALA GLU LEU PRO ALA ARG HIS GLU SEQRES 32 A 415 ARG GLN GLU PRO VAL GLY ASP ARG PRO ASN GLY GLY SEQRES 1 B 415 MET THR THR GLN THR THR PRO ALA HIS ILE ALA MET PHE SEQRES 2 B 415 SER ILE ALA ALA HIS GLY HIS VAL ASN PRO SER LEU GLU SEQRES 3 B 415 VAL ILE ARG GLU LEU VAL ALA ARG GLY HIS ARG VAL THR SEQRES 4 B 415 TYR ALA ILE PRO PRO VAL PHE ALA ASP LYS VAL ALA ALA SEQRES 5 B 415 THR GLY PRO ARG PRO VAL LEU TYR HIS SER THR LEU PRO SEQRES 6 B 415 GLY PRO ASP ALA ASP PRO GLU ALA TRP GLY SER THR LEU SEQRES 7 B 415 LEU ASP ASN VAL GLU PRO PHE LEU ASN ASP ALA ILE GLN SEQRES 8 B 415 ALA LEU PRO GLN LEU ALA ASP ALA TYR ALA ASP ASP ILE SEQRES 9 B 415 PRO ASP LEU VAL LEU HIS ASP ILE THR SER TYR PRO ALA SEQRES 10 B 415 ARG VAL LEU ALA ARG ARG TRP GLY VAL PRO ALA VAL SER SEQRES 11 B 415 LEU SER PRO ASN LEU VAL ALA TRP LYS GLY TYR GLU GLU SEQRES 12 B 415 GLU VAL ALA GLU PRO MET TRP ARG GLU PRO ARG GLN THR SEQRES 13 B 415 GLU ARG GLY ARG ALA TYR TYR ALA ARG PHE GLU ALA TRP SEQRES 14 B 415 LEU LYS GLU ASN GLY ILE THR GLU HIS PRO ASP THR PHE SEQRES 15 B 415 ALA SER HIS PRO PRO ARG SER LEU VAL LEU ILE PRO LYS SEQRES 16 B 415 ALA LEU GLN PRO HIS ALA ASP ARG VAL ASP GLU ASP VAL SEQRES 17 B 415 TYR THR PHE VAL GLY ALA CYS GLN GLY ASP ARG ALA GLU SEQRES 18 B 415 GLU GLY GLY TRP GLN ARG PRO ALA GLY ALA GLU LYS VAL SEQRES 19 B 415 VAL LEU VAL SER LEU GLY SER ALA PHE THR LYS GLN PRO SEQRES 20 B 415 ALA PHE TYR ARG GLU CYS VAL ARG ALA PHE GLY ASN LEU SEQRES 21 B 415 PRO GLY TRP HIS LEU VAL LEU GLN ILE GLY ARG LYS VAL SEQRES 22 B 415 THR PRO ALA GLU LEU GLY GLU LEU PRO ASP ASN VAL GLU SEQRES 23 B 415 VAL HIS ASP TRP VAL PRO GLN LEU ALA ILE LEU ARG GLN SEQRES 24 B 415 ALA ASP LEU PHE VAL THR HIS ALA GLY ALA GLY GLY SER SEQRES 25 B 415 GLN GLU GLY LEU ALA THR ALA THR PRO MET ILE ALA VAL SEQRES 26 B 415 PRO GLN ALA VAL ASP GLN PHE GLY ASN ALA ASP MET LEU SEQRES 27 B 415 GLN GLY LEU GLY VAL ALA ARG LYS LEU ALA THR GLU GLU SEQRES 28 B 415 ALA THR ALA ASP LEU LEU ARG GLU THR ALA LEU ALA LEU SEQRES 29 B 415 VAL ASP ASP PRO GLU VAL ALA ARG ARG LEU ARG ARG ILE SEQRES 30 B 415 GLN ALA GLU MET ALA GLN GLU GLY GLY THR ARG ARG ALA SEQRES 31 B 415 ALA ASP LEU ILE GLU ALA GLU LEU PRO ALA ARG HIS GLU SEQRES 32 B 415 ARG GLN GLU PRO VAL GLY ASP ARG PRO ASN GLY GLY HET ERY A1400 51 HET UDP A1401 25 HET ERY B1399 51 HET UDP B1400 25 HET MG B1401 1 HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM ERY ERYTHROMYCIN A HETNAM MG MAGNESIUM ION FORMUL 3 UDP 2(C9 H14 N2 O12 P2) FORMUL 4 ERY 2(C37 H67 N O13) FORMUL 5 MG MG 2+ FORMUL 6 HOH *604(H2 O1) HELIX 1 1 ALA A 16 ASN A 21 1 6 HELIX 2 2 SER A 23 ARG A 33 1 11 HELIX 3 3 PRO A 42 VAL A 44 5 3 HELIX 4 4 PHE A 45 ALA A 51 1 7 HELIX 5 5 ASP A 69 GLY A 74 5 6 HELIX 6 6 THR A 76 ALA A 100 1 25 HELIX 7 7 SER A 113 GLY A 124 1 12 HELIX 8 8 GLY A 139 VAL A 144 1 6 HELIX 9 9 VAL A 144 ASN A 172 1 29 HELIX 10 10 HIS A 177 HIS A 184 1 8 HELIX 11 11 PRO A 193 GLN A 197 5 5 HELIX 12 12 HIS A 199 VAL A 203 5 5 HELIX 13 13 GLN A 245 GLY A 257 1 13 HELIX 14 14 THR A 273 GLY A 278 5 6 HELIX 15 15 PRO A 291 ARG A 297 1 7 HELIX 16 16 GLY A 307 THR A 317 1 11 HELIX 17 17 ALA A 327 ASP A 329 5 3 HELIX 18 18 GLN A 330 LEU A 340 1 11 HELIX 19 19 ALA A 347 ALA A 351 5 5 HELIX 20 20 THR A 352 ASP A 366 1 15 HELIX 21 21 ASP A 366 GLY A 384 1 19 HELIX 22 22 GLY A 384 ALA A 395 1 12 HELIX 23 23 ALA B 16 HIS B 19 5 4 HELIX 24 24 VAL B 20 ARG B 33 1 14 HELIX 25 25 PRO B 42 VAL B 44 5 3 HELIX 26 26 PHE B 45 ALA B 51 1 7 HELIX 27 27 ASP B 69 GLY B 74 5 6 HELIX 28 28 THR B 76 ALA B 100 1 25 HELIX 29 29 SER B 113 GLY B 124 1 12 HELIX 30 30 GLY B 139 VAL B 144 1 6 HELIX 31 31 VAL B 144 ARG B 150 1 7 HELIX 32 32 GLU B 151 GLN B 154 5 4 HELIX 33 33 THR B 155 ASN B 172 1 18 HELIX 34 34 HIS B 177 HIS B 184 1 8 HELIX 35 35 PRO B 193 GLN B 197 5 5 HELIX 36 36 HIS B 199 VAL B 203 5 5 HELIX 37 37 ARG B 218 GLY B 222 5 5 HELIX 38 38 GLN B 245 GLY B 257 1 13 HELIX 39 39 THR B 273 GLY B 278 5 6 HELIX 40 40 PRO B 291 ARG B 297 1 7 HELIX 41 41 GLY B 307 THR B 317 1 11 HELIX 42 42 ASP B 329 LEU B 340 1 12 HELIX 43 43 ALA B 347 ALA B 351 5 5 HELIX 44 44 THR B 352 ASP B 366 1 15 HELIX 45 45 ASP B 366 GLY B 384 1 19 HELIX 46 46 GLY B 384 ALA B 395 1 12 SHEET 1 AA 7 ARG A 55 LEU A 58 0 SHEET 2 AA 7 ARG A 36 ILE A 41 1 O VAL A 37 N ARG A 55 SHEET 3 AA 7 HIS A 8 PHE A 12 1 O ILE A 9 N THR A 38 SHEET 4 AA 7 LEU A 106 ASP A 110 1 O LEU A 106 N ALA A 10 SHEET 5 AA 7 ALA A 127 SER A 131 1 O VAL A 128 N HIS A 109 SHEET 6 AA 7 SER A 188 VAL A 190 1 O LEU A 189 N SER A 131 SHEET 7 AA 7 TYR A 208 PHE A 210 1 O THR A 209 N VAL A 190 SHEET 1 AB 6 VAL A 284 HIS A 287 0 SHEET 2 AB 6 TRP A 262 GLN A 267 1 O LEU A 264 N GLU A 285 SHEET 3 AB 6 LYS A 232 SER A 237 1 O LYS A 232 N HIS A 263 SHEET 4 AB 6 LEU A 301 THR A 304 1 O LEU A 301 N LEU A 235 SHEET 5 AB 6 MET A 321 ALA A 323 1 O ILE A 322 N THR A 304 SHEET 6 AB 6 ALA A 343 LYS A 345 1 O ARG A 344 N ALA A 323 SHEET 1 BA 7 ARG B 55 LEU B 58 0 SHEET 2 BA 7 ARG B 36 ILE B 41 1 O VAL B 37 N ARG B 55 SHEET 3 BA 7 HIS B 8 PHE B 12 1 O ILE B 9 N THR B 38 SHEET 4 BA 7 LEU B 106 ASP B 110 1 O LEU B 106 N ALA B 10 SHEET 5 BA 7 ALA B 127 SER B 131 1 O VAL B 128 N HIS B 109 SHEET 6 BA 7 SER B 188 VAL B 190 1 O LEU B 189 N SER B 131 SHEET 7 BA 7 TYR B 208 PHE B 210 1 O THR B 209 N VAL B 190 SHEET 1 BB 6 VAL B 284 HIS B 287 0 SHEET 2 BB 6 TRP B 262 GLN B 267 1 O LEU B 264 N GLU B 285 SHEET 3 BB 6 LYS B 232 SER B 237 1 O LYS B 232 N HIS B 263 SHEET 4 BB 6 LEU B 301 THR B 304 1 O LEU B 301 N LEU B 235 SHEET 5 BB 6 MET B 321 ALA B 323 1 O ILE B 322 N THR B 304 SHEET 6 BB 6 ALA B 343 LYS B 345 1 O ARG B 344 N ALA B 323 LINK MG MG B1401 O HOH B2216 1555 1555 2.38 LINK MG MG B1401 O THR B 317 1555 1555 2.16 LINK MG MG B1401 O HOH B2213 1555 1555 2.25 LINK MG MG B1401 O HOH B2212 1555 1555 2.06 LINK MG MG B1401 O HOH B2215 1555 1555 2.05 SITE 1 AC1 12 HIS A 19 TRP A 73 ASN A 80 VAL A 81 SITE 2 AC1 12 ASN A 133 ALA A 182 SER A 183 ASP A 329 SITE 3 AC1 12 HOH A2308 HOH A2309 HOH A2310 HOH A2312 SITE 1 AC2 18 GLY A 239 SER A 240 ALA A 241 GLN A 267 SITE 2 AC2 18 TRP A 289 VAL A 290 GLN A 292 HIS A 305 SITE 3 AC2 18 ALA A 308 GLY A 309 GLY A 310 GLU A 313 SITE 4 AC2 18 HOH A2214 HOH A2313 HOH A2314 HOH A2315 SITE 5 AC2 18 HOH A2316 HOH A2317 SITE 1 AC3 14 HIS B 19 TRP B 73 ASN B 80 PHE B 84 SITE 2 AC3 14 ILE B 111 ASN B 133 LEU B 134 TYR B 140 SITE 3 AC3 14 ALA B 182 SER B 183 HOH B2108 HOH B2280 SITE 4 AC3 14 HOH B2281 HOH B2282 SITE 1 AC4 17 ARG B 218 GLY B 239 SER B 240 GLN B 267 SITE 2 AC4 17 TRP B 289 VAL B 290 GLN B 292 HIS B 305 SITE 3 AC4 17 GLY B 307 ALA B 308 GLY B 309 GLY B 310 SITE 4 AC4 17 GLU B 313 HOH B2182 HOH B2283 HOH B2287 SITE 5 AC4 17 HOH B2288 SITE 1 AC5 5 THR B 317 HOH B2212 HOH B2213 HOH B2215 SITE 2 AC5 5 HOH B2216 CRYST1 72.718 65.778 91.940 90.00 100.42 90.00 P 1 21 1 4 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 0.013752 0.000000 0.002529 0.00000 SCALE2 0.000000 0.015203 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011059 0.00000