HEADER TRANSFERASE 06-DEC-11 3UYL TITLE SPINOSYN RHAMNOSYLTRANSFERASE SPNG COMPLEXED WITH THYMIDINE TITLE 2 DIPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NDP-RHAMNOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1-386; COMPND 5 SYNONYM: SPNG; COMPND 6 EC: 2.4.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROPOLYSPORA SPINOSA; SOURCE 3 ORGANISM_TAXID: 60894; SOURCE 4 GENE: SPNG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.A.ISIORHO,H.-W.LIU,A.T.KEATINGE-CLAY REVDAT 5 13-SEP-23 3UYL 1 HETSYN REVDAT 4 29-JUL-20 3UYL 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 24-JAN-18 3UYL 1 AUTHOR REVDAT 2 29-FEB-12 3UYL 1 JRNL REVDAT 1 15-FEB-12 3UYL 0 JRNL AUTH E.A.ISIORHO,H.W.LIU,A.T.KEATINGE-CLAY JRNL TITL STRUCTURAL STUDIES OF THE SPINOSYN RHAMNOSYLTRANSFERASE, JRNL TITL 2 SPNG. JRNL REF BIOCHEMISTRY V. 51 1213 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22283226 JRNL DOI 10.1021/BI201860Q REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC VERSION: 5.5.0072 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 57920 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3104 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) : 1.86 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4076 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.4190 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.4550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5533 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 417 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : -0.01000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.01000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.189 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.182 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.337 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.900 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.840 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5736 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 12 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7880 ; 2.141 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 20 ; 1.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 6.616 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;35.257 ;23.289 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 814 ;15.544 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.658 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 918 ; 0.134 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4406 ; 0.012 ; 0.022 REMARK 3 GENERAL PLANES OTHERS (A): 4 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3UYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000069371. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : ASYMMETRIC CUT SINGLE CRYSTAL REMARK 200 SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57920 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 24.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER MR REMARK 200 STARTING MODEL: PDB ENTRY 3TSA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% W/V PEG3350, 12.5-13.5% W/V REMARK 280 GLUCOSE, 1% V/V GLYCEROL, 0.1 M MAGNESIUM FORMATE, 0.1 M SODIUM REMARK 280 CACODYLATE, PH 6.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 GLY A 55 REMARK 465 ASN A 56 REMARK 465 ASP A 57 REMARK 465 ARG A 58 REMARK 465 THR A 59 REMARK 465 GLY A 60 REMARK 465 ASP A 61 REMARK 465 THR A 62 REMARK 465 GLY A 63 REMARK 465 GLY A 64 REMARK 465 THR A 65 REMARK 465 THR A 66 REMARK 465 GLN A 67 REMARK 465 LEU A 68 REMARK 465 ALA A 386 REMARK 465 HIS B 0 REMARK 465 GLY B 55 REMARK 465 ASN B 56 REMARK 465 ASP B 57 REMARK 465 ARG B 58 REMARK 465 THR B 59 REMARK 465 GLY B 60 REMARK 465 ASP B 61 REMARK 465 THR B 62 REMARK 465 GLY B 63 REMARK 465 GLY B 64 REMARK 465 THR B 65 REMARK 465 THR B 66 REMARK 465 GLN B 67 REMARK 465 LEU B 68 REMARK 465 THR B 385 REMARK 465 ALA B 386 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 A 633 O HOH A 683 2.14 REMARK 500 O HOH B 548 O HOH B 695 2.16 REMARK 500 OE1 GLU A 287 O HOH A 656 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 597 O HOH B 708 1556 1.57 REMARK 500 O HOH A 703 O HOH B 704 1556 1.80 REMARK 500 O HOH A 703 O HOH B 705 1556 1.94 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 TRP A 112 CE2 TRP A 112 CD2 0.089 REMARK 500 TRP A 142 CE2 TRP A 142 CD2 0.077 REMARK 500 TRP B 142 CE2 TRP B 142 CD2 0.074 REMARK 500 HIS B 166 CG HIS B 166 CD2 0.065 REMARK 500 HIS B 260 CG HIS B 260 CD2 0.061 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 PRO A 146 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 239 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 MET A 372 CG - SD - CE ANGL. DEV. = -14.5 DEGREES REMARK 500 LEU B 133 CB - CG - CD1 ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG B 141 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 PRO B 172 C - N - CA ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG B 214 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU B 378 CA - CB - CG ANGL. DEV. = -20.0 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 PRO A 9 48.89 -71.54 REMARK 500 THR A 215 -166.26 -115.23 REMARK 500 ASP A 266 49.99 38.39 REMARK 500 SER A 276 58.78 28.11 REMARK 500 PHE A 315 -122.42 54.04 REMARK 500 PRO B 9 49.49 -69.94 REMARK 500 ILE B 125 -38.10 -35.63 REMARK 500 GLN B 192 119.83 -31.82 REMARK 500 PHE B 282 -14.13 -144.64 REMARK 500 PHE B 315 -125.12 49.60 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 A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 541 O REMARK 620 2 HOH A 582 O 90.7 REMARK 620 3 HOH A 597 O 75.1 80.6 REMARK 620 4 HOH A 703 O 131.0 98.3 153.9 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TSA RELATED DB: PDB REMARK 900 SPINOSYN RHAMNOSYLTRANSFERASE SPNG REMARK 900 RELATED ID: 3UYK RELATED DB: PDB REMARK 900 SPINOSYN RHAMNOSYLTRANSFERASE SPNG COMPLEXED WITH SPINOSYN AGLYCONE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AUTHORS STATE THAT RESIDUE ALA 360 IS CORRECT. DBREF 3UYL A 1 386 UNP Q9ALM8 Q9ALM8_9PSEU 1 386 DBREF 3UYL B 1 386 UNP Q9ALM8 Q9ALM8_9PSEU 1 386 SEQADV 3UYL HIS A 0 UNP Q9ALM8 EXPRESSION TAG SEQADV 3UYL ALA A 360 UNP Q9ALM8 SER 360 SEE REMARK 999 SEQADV 3UYL HIS B 0 UNP Q9ALM8 EXPRESSION TAG SEQADV 3UYL ALA B 360 UNP Q9ALM8 SER 360 SEE REMARK 999 SEQRES 1 A 387 HIS MET ARG VAL LEU VAL VAL PRO LEU PRO TYR PRO THR SEQRES 2 A 387 HIS LEU MET ALA MET VAL PRO LEU CYS TRP ALA LEU GLN SEQRES 3 A 387 ALA SER GLY HIS GLU VAL LEU ILE ALA ALA PRO PRO GLU SEQRES 4 A 387 LEU GLN ALA THR ALA HIS GLY ALA GLY LEU THR THR ALA SEQRES 5 A 387 GLY ILE ARG GLY ASN ASP ARG THR GLY ASP THR GLY GLY SEQRES 6 A 387 THR THR GLN LEU ARG PHE PRO ASN PRO ALA PHE GLY GLN SEQRES 7 A 387 ARG ASP THR GLU ALA GLY ARG GLN LEU TRP GLU GLN THR SEQRES 8 A 387 ALA SER ASN VAL ALA GLN SER SER LEU ASP GLN LEU PRO SEQRES 9 A 387 GLU TYR LEU ARG LEU ALA GLU ALA TRP ARG PRO SER VAL SEQRES 10 A 387 LEU LEU VAL ASP VAL CYS ALA LEU ILE GLY ARG VAL LEU SEQRES 11 A 387 GLY GLY LEU LEU ASP LEU PRO VAL VAL LEU HIS ARG TRP SEQRES 12 A 387 GLY VAL ASP PRO THR ALA GLY PRO PHE SER ASP ARG ALA SEQRES 13 A 387 HIS GLU LEU LEU ASP PRO VAL CYS ARG HIS HIS GLY LEU SEQRES 14 A 387 THR GLY LEU PRO THR PRO GLU LEU ILE LEU ASP PRO CYS SEQRES 15 A 387 PRO PRO SER LEU GLN ALA SER ASP ALA PRO GLN GLY ALA SEQRES 16 A 387 PRO VAL GLN TYR VAL PRO TYR ASN GLY SER GLY ALA PHE SEQRES 17 A 387 PRO ALA TRP GLY ALA ALA ARG THR SER ALA ARG ARG VAL SEQRES 18 A 387 CYS ILE CYS MET GLY ARG MET VAL LEU ASN ALA THR GLY SEQRES 19 A 387 PRO ALA PRO LEU LEU ARG ALA VAL ALA ALA ALA THR GLU SEQRES 20 A 387 LEU PRO GLY VAL GLU ALA VAL ILE ALA VAL PRO PRO GLU SEQRES 21 A 387 HIS ARG ALA LEU LEU THR ASP LEU PRO ASP ASN ALA ARG SEQRES 22 A 387 ILE ALA GLU SER VAL PRO LEU ASN LEU PHE LEU ARG THR SEQRES 23 A 387 CYS GLU LEU VAL ILE CYS ALA GLY GLY SER GLY THR ALA SEQRES 24 A 387 PHE THR ALA THR ARG LEU GLY ILE PRO GLN LEU VAL LEU SEQRES 25 A 387 PRO GLN TYR PHE ASP GLN PHE ASP TYR ALA ARG ASN LEU SEQRES 26 A 387 ALA ALA ALA GLY ALA GLY ILE CYS LEU PRO ASP GLU GLN SEQRES 27 A 387 ALA GLN SER ASP HIS GLU GLN PHE THR ASP SER ILE ALA SEQRES 28 A 387 THR VAL LEU GLY ASP THR GLY PHE ALA ALA ALA ALA ILE SEQRES 29 A 387 LYS LEU SER ASP GLU ILE THR ALA MET PRO HIS PRO ALA SEQRES 30 A 387 ALA LEU VAL ARG THR LEU GLU ASN THR ALA SEQRES 1 B 387 HIS MET ARG VAL LEU VAL VAL PRO LEU PRO TYR PRO THR SEQRES 2 B 387 HIS LEU MET ALA MET VAL PRO LEU CYS TRP ALA LEU GLN SEQRES 3 B 387 ALA SER GLY HIS GLU VAL LEU ILE ALA ALA PRO PRO GLU SEQRES 4 B 387 LEU GLN ALA THR ALA HIS GLY ALA GLY LEU THR THR ALA SEQRES 5 B 387 GLY ILE ARG GLY ASN ASP ARG THR GLY ASP THR GLY GLY SEQRES 6 B 387 THR THR GLN LEU ARG PHE PRO ASN PRO ALA PHE GLY GLN SEQRES 7 B 387 ARG ASP THR GLU ALA GLY ARG GLN LEU TRP GLU GLN THR SEQRES 8 B 387 ALA SER ASN VAL ALA GLN SER SER LEU ASP GLN LEU PRO SEQRES 9 B 387 GLU TYR LEU ARG LEU ALA GLU ALA TRP ARG PRO SER VAL SEQRES 10 B 387 LEU LEU VAL ASP VAL CYS ALA LEU ILE GLY ARG VAL LEU SEQRES 11 B 387 GLY GLY LEU LEU ASP LEU PRO VAL VAL LEU HIS ARG TRP SEQRES 12 B 387 GLY VAL ASP PRO THR ALA GLY PRO PHE SER ASP ARG ALA SEQRES 13 B 387 HIS GLU LEU LEU ASP PRO VAL CYS ARG HIS HIS GLY LEU SEQRES 14 B 387 THR GLY LEU PRO THR PRO GLU LEU ILE LEU ASP PRO CYS SEQRES 15 B 387 PRO PRO SER LEU GLN ALA SER ASP ALA PRO GLN GLY ALA SEQRES 16 B 387 PRO VAL GLN TYR VAL PRO TYR ASN GLY SER GLY ALA PHE SEQRES 17 B 387 PRO ALA TRP GLY ALA ALA ARG THR SER ALA ARG ARG VAL SEQRES 18 B 387 CYS ILE CYS MET GLY ARG MET VAL LEU ASN ALA THR GLY SEQRES 19 B 387 PRO ALA PRO LEU LEU ARG ALA VAL ALA ALA ALA THR GLU SEQRES 20 B 387 LEU PRO GLY VAL GLU ALA VAL ILE ALA VAL PRO PRO GLU SEQRES 21 B 387 HIS ARG ALA LEU LEU THR ASP LEU PRO ASP ASN ALA ARG SEQRES 22 B 387 ILE ALA GLU SER VAL PRO LEU ASN LEU PHE LEU ARG THR SEQRES 23 B 387 CYS GLU LEU VAL ILE CYS ALA GLY GLY SER GLY THR ALA SEQRES 24 B 387 PHE THR ALA THR ARG LEU GLY ILE PRO GLN LEU VAL LEU SEQRES 25 B 387 PRO GLN TYR PHE ASP GLN PHE ASP TYR ALA ARG ASN LEU SEQRES 26 B 387 ALA ALA ALA GLY ALA GLY ILE CYS LEU PRO ASP GLU GLN SEQRES 27 B 387 ALA GLN SER ASP HIS GLU GLN PHE THR ASP SER ILE ALA SEQRES 28 B 387 THR VAL LEU GLY ASP THR GLY PHE ALA ALA ALA ALA ILE SEQRES 29 B 387 LYS LEU SER ASP GLU ILE THR ALA MET PRO HIS PRO ALA SEQRES 30 B 387 ALA LEU VAL ARG THR LEU GLU ASN THR ALA HET TYD A 401 25 HET MG A 402 1 HET TYD B 401 25 HET GLC B 402 12 HET MG B 403 1 HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 TYD 2(C10 H16 N2 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 6 GLC C6 H12 O6 FORMUL 8 HOH *417(H2 O) HELIX 1 1 TYR A 10 ALA A 16 1 7 HELIX 2 2 MET A 17 SER A 27 1 11 HELIX 3 3 PRO A 36 GLU A 38 5 3 HELIX 4 4 LEU A 39 ALA A 46 1 8 HELIX 5 5 ASN A 72 GLN A 77 5 6 HELIX 6 6 THR A 80 ARG A 113 1 34 HELIX 7 7 ALA A 123 LEU A 133 1 11 HELIX 8 8 GLY A 149 HIS A 166 1 18 HELIX 9 9 PRO A 182 GLN A 186 5 5 HELIX 10 10 PRO A 208 ALA A 212 5 5 HELIX 11 11 GLY A 225 GLY A 233 1 9 HELIX 12 12 PRO A 234 LEU A 247 1 14 HELIX 13 13 PRO A 257 LEU A 264 5 8 HELIX 14 14 PRO A 278 CYS A 286 5 9 HELIX 15 15 GLY A 294 LEU A 304 1 11 HELIX 16 16 ASP A 316 ALA A 327 1 12 HELIX 17 17 ASP A 335 SER A 340 1 6 HELIX 18 18 ASP A 341 GLY A 354 1 14 HELIX 19 19 THR A 356 ALA A 371 1 16 HELIX 20 20 HIS A 374 THR A 385 1 12 HELIX 21 21 TYR B 10 ALA B 16 1 7 HELIX 22 22 MET B 17 SER B 27 1 11 HELIX 23 23 PRO B 36 ALA B 46 1 11 HELIX 24 24 ASN B 72 GLN B 77 5 6 HELIX 25 25 THR B 80 ARG B 113 1 34 HELIX 26 26 ALA B 123 ASP B 134 1 12 HELIX 27 27 GLY B 149 HIS B 166 1 18 HELIX 28 28 PRO B 182 GLN B 186 5 5 HELIX 29 29 PRO B 208 ALA B 212 5 5 HELIX 30 30 GLY B 225 GLY B 233 1 9 HELIX 31 31 PRO B 234 LEU B 247 1 14 HELIX 32 32 PRO B 257 LEU B 264 5 8 HELIX 33 33 PRO B 278 CYS B 286 5 9 HELIX 34 34 GLY B 294 LEU B 304 1 11 HELIX 35 35 ASP B 316 ALA B 327 1 12 HELIX 36 36 ASP B 335 SER B 340 1 6 HELIX 37 37 ASP B 341 ASP B 355 1 15 HELIX 38 38 THR B 356 ALA B 371 1 16 HELIX 39 39 HIS B 374 ASN B 384 1 11 SHEET 1 A 8 ALA A 194 PRO A 195 0 SHEET 2 A 8 LEU A 176 ASP A 179 1 N ILE A 177 O ALA A 194 SHEET 3 A 8 VAL A 137 HIS A 140 1 N LEU A 139 O LEU A 178 SHEET 4 A 8 VAL A 116 ASP A 120 1 N LEU A 117 O VAL A 138 SHEET 5 A 8 ARG A 2 VAL A 6 1 N VAL A 6 O LEU A 118 SHEET 6 A 8 GLU A 30 ALA A 35 1 O GLU A 30 N VAL A 3 SHEET 7 A 8 THR A 49 GLY A 52 1 O THR A 49 N ILE A 33 SHEET 8 A 8 GLY B 205 ALA B 206 1 O GLY B 205 N THR A 50 SHEET 1 B 8 GLY A 205 ALA A 206 0 SHEET 2 B 8 THR B 49 GLY B 52 1 O THR B 50 N GLY A 205 SHEET 3 B 8 GLU B 30 ALA B 35 1 N ILE B 33 O ALA B 51 SHEET 4 B 8 ARG B 2 VAL B 6 1 N VAL B 5 O LEU B 32 SHEET 5 B 8 VAL B 116 ASP B 120 1 O LEU B 118 N VAL B 6 SHEET 6 B 8 VAL B 137 HIS B 140 1 O VAL B 138 N LEU B 117 SHEET 7 B 8 LEU B 176 ASP B 179 1 O LEU B 178 N LEU B 139 SHEET 8 B 8 ALA B 194 PRO B 195 1 O ALA B 194 N ILE B 177 SHEET 1 C 6 ALA A 271 GLU A 275 0 SHEET 2 C 6 VAL A 250 VAL A 256 1 N ILE A 254 O ARG A 272 SHEET 3 C 6 ARG A 218 CYS A 223 1 N VAL A 220 O VAL A 253 SHEET 4 C 6 LEU A 288 CYS A 291 1 O ILE A 290 N CYS A 221 SHEET 5 C 6 GLN A 308 VAL A 310 1 O LEU A 309 N VAL A 289 SHEET 6 C 6 GLY A 330 CYS A 332 1 O ILE A 331 N VAL A 310 SHEET 1 D 6 ARG B 272 GLU B 275 0 SHEET 2 D 6 VAL B 250 VAL B 256 1 N ILE B 254 O ARG B 272 SHEET 3 D 6 ARG B 218 CYS B 223 1 N VAL B 220 O VAL B 253 SHEET 4 D 6 LEU B 288 CYS B 291 1 O ILE B 290 N CYS B 221 SHEET 5 D 6 GLN B 308 VAL B 310 1 O LEU B 309 N VAL B 289 SHEET 6 D 6 GLY B 330 CYS B 332 1 O ILE B 331 N VAL B 310 LINK MG MG A 402 O HOH A 541 1555 1555 2.10 LINK MG MG A 402 O HOH A 582 1555 1555 1.95 LINK MG MG A 402 O HOH A 597 1555 1555 2.17 LINK MG MG A 402 O HOH A 703 1555 1555 1.92 CISPEP 1 PHE A 70 PRO A 71 0 -9.17 CISPEP 2 PHE B 70 PRO B 71 0 -0.10 CRYST1 54.152 57.629 68.203 81.63 73.79 85.74 P 1 2 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 0.018467 -0.001376 -0.005234 0.00000 SCALE2 0.000000 0.017400 -0.002288 0.00000 SCALE3 0.000000 0.000000 0.015401 0.00000