HEADER TRANSFERASE 18-MAY-12 4F96 TITLE CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN COMPLEX TITLE 2 WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: VLDE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: PSEUDO-GLYCOSYLTRANSFERASE; COMPND 5 EC: 2.4.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES HYGROSCOPICUS SUBSP. LIMONEUS; SOURCE 3 ORGANISM_TAXID: 264445; SOURCE 4 GENE: VLDE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TWIN ROSSMAN FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.CAVALIER,Y.-S.YIM,S.ASAMIZU,D.NEAU,K.H.ALMABRUK,T.MAHMUD,Y.-H.LEE REVDAT 2 28-FEB-24 4F96 1 REMARK REVDAT 1 17-OCT-12 4F96 0 JRNL AUTH M.C.CAVALIER,Y.S.YIM,S.ASAMIZU,D.NEAU,K.H.ALMABRUK,T.MAHMUD, JRNL AUTH 2 Y.H.LEE JRNL TITL MECHANISTIC INSIGHTS INTO VALIDOXYLAMINE A 7'-PHOSPHATE JRNL TITL 2 SYNTHESIS BY VLDE USING THE STRUCTURE OF THE ENTIRE PRODUCT JRNL TITL 3 COMPLEX. JRNL REF PLOS ONE V. 7 44934 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 23028689 JRNL DOI 10.1371/JOURNAL.PONE.0044934 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.52 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 51924 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2645 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 37.5295 - 5.7361 0.99 2615 146 0.1832 0.1881 REMARK 3 2 5.7361 - 4.5554 1.00 2631 138 0.1656 0.1722 REMARK 3 3 4.5554 - 3.9803 1.00 2572 149 0.1486 0.1721 REMARK 3 4 3.9803 - 3.6167 1.00 2629 126 0.1720 0.1919 REMARK 3 5 3.6167 - 3.3577 1.00 2559 155 0.1826 0.2030 REMARK 3 6 3.3577 - 3.1598 1.00 2606 137 0.2005 0.2057 REMARK 3 7 3.1598 - 3.0016 1.00 2603 129 0.2077 0.2641 REMARK 3 8 3.0016 - 2.8710 1.00 2627 141 0.2008 0.2365 REMARK 3 9 2.8710 - 2.7605 1.00 2565 145 0.1982 0.1928 REMARK 3 10 2.7605 - 2.6653 1.00 2590 130 0.1987 0.2206 REMARK 3 11 2.6653 - 2.5820 1.00 2624 135 0.2088 0.2118 REMARK 3 12 2.5820 - 2.5082 1.00 2570 134 0.2141 0.2617 REMARK 3 13 2.5082 - 2.4422 1.00 2603 143 0.2133 0.2435 REMARK 3 14 2.4422 - 2.3826 1.00 2568 137 0.2252 0.2434 REMARK 3 15 2.3826 - 2.3285 1.00 2594 136 0.2193 0.2456 REMARK 3 16 2.3285 - 2.2789 1.00 2541 153 0.2386 0.2365 REMARK 3 17 2.2789 - 2.2333 1.00 2611 141 0.2429 0.3068 REMARK 3 18 2.2333 - 2.1912 1.00 2626 135 0.2395 0.3187 REMARK 3 19 2.1912 - 2.1520 0.98 2545 135 0.2450 0.2431 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 35.87 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.00340 REMARK 3 B22 (A**2) : -4.54160 REMARK 3 B33 (A**2) : -0.46190 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.25900 REMARK 3 B23 (A**2) : 0.00000 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 : 0.012 7610 REMARK 3 ANGLE : 1.297 10384 REMARK 3 CHIRALITY : 0.083 1134 REMARK 3 PLANARITY : 0.007 1374 REMARK 3 DIHEDRAL : 14.833 2758 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 : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN 'B' AND (RESSEQ 4:261 OR RESSEQ REMARK 3 269:481 ) AND (NOT ELEMENT H) AND (NOT REMARK 3 ELEMENT D) REMARK 3 SELECTION : CHAIN 'A' AND (RESSEQ 4:261 OR RESSEQ REMARK 3 269:481 ) AND (NOT ELEMENT H) AND (NOT REMARK 3 ELEMENT D) REMARK 3 ATOM PAIRS NUMBER : 3681 REMARK 3 RMSD : 0.314 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F96 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X6A 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 : SI(111) CHANNEL CUT REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51924 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 37.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 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) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, PH 8.0, 30-35% REMARK 280 PEG3350, 3 MM GDP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 60.57550 REMARK 290 SMTRY3 2 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: 5770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B 1 REMARK 465 THR B 2 REMARK 465 GLY B 3 REMARK 465 THR B 263 REMARK 465 LEU B 264 REMARK 465 ASP B 265 REMARK 465 GLY B 266 REMARK 465 ARG B 267 REMARK 465 ASN B 268 REMARK 465 ALA B 482 REMARK 465 GLU B 483 REMARK 465 ARG B 484 REMARK 465 PHE B 485 REMARK 465 ASP B 486 REMARK 465 THR B 487 REMARK 465 ALA B 488 REMARK 465 PRO B 489 REMARK 465 ALA B 490 REMARK 465 VAL B 491 REMARK 465 SER B 492 REMARK 465 THR B 493 REMARK 465 ARG B 494 REMARK 465 ALA B 495 REMARK 465 ASP B 496 REMARK 465 LEU B 497 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 THR A 263 REMARK 465 LEU A 264 REMARK 465 ASP A 265 REMARK 465 GLY A 266 REMARK 465 ARG A 267 REMARK 465 ASN A 268 REMARK 465 ALA A 482 REMARK 465 GLU A 483 REMARK 465 ARG A 484 REMARK 465 PHE A 485 REMARK 465 ASP A 486 REMARK 465 THR A 487 REMARK 465 ALA A 488 REMARK 465 PRO A 489 REMARK 465 ALA A 490 REMARK 465 VAL A 491 REMARK 465 SER A 492 REMARK 465 THR A 493 REMARK 465 ARG A 494 REMARK 465 ALA A 495 REMARK 465 ASP A 496 REMARK 465 LEU A 497 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 739 O HOH A 743 1.85 REMARK 500 O HOH A 777 O HOH A 783 1.85 REMARK 500 O HOH B 732 O HOH B 734 1.88 REMARK 500 NH2 ARG A 456 O HOH A 729 1.88 REMARK 500 NH2 ARG A 192 O HOH A 670 1.90 REMARK 500 SD MET A 255 O HOH A 748 1.90 REMARK 500 O HOH A 672 O HOH A 763 1.91 REMARK 500 O HOH B 760 O HOH B 793 1.91 REMARK 500 O HOH A 787 O HOH A 789 1.93 REMARK 500 CB ASP A 233 O HOH A 739 1.95 REMARK 500 O HOH A 739 O HOH A 791 1.96 REMARK 500 O HOH B 748 O HOH B 771 1.98 REMARK 500 NE ARG A 125 O HOH A 721 2.01 REMARK 500 NH1 ARG A 450 O HOH A 761 2.01 REMARK 500 NH1 ARG B 246 O HOH B 775 2.01 REMARK 500 OD1 ASP B 360 O HOH B 736 2.03 REMARK 500 OD1 ASP B 360 O HOH B 755 2.08 REMARK 500 O HOH A 755 O HOH A 782 2.13 REMARK 500 O HOH A 786 O HOH A 795 2.14 REMARK 500 O HOH B 749 O HOH B 767 2.16 REMARK 500 OE1 GLU A 170 O HOH A 724 2.16 REMARK 500 CE MET A 255 O HOH A 748 2.17 REMARK 500 O HOH B 604 O HOH B 720 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 61 O GLY A 310 2554 2.16 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 GLN B 467 CD GLN B 467 OE1 -0.148 REMARK 500 GLN B 467 CD GLN B 467 NE2 -0.179 REMARK 500 GLN A 467 CD GLN A 467 OE1 -0.158 REMARK 500 GLN A 467 CD GLN A 467 NE2 -0.178 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 61 NE - CZ - NH1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 61 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 450 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 450 NE - CZ - NH2 ANGL. DEV. = 3.4 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 LEU B 103 -87.07 -145.08 REMARK 500 ARG B 114 -49.15 73.53 REMARK 500 ASP B 158 145.00 94.36 REMARK 500 ASP B 360 142.62 -177.33 REMARK 500 ASN B 379 42.45 -109.33 REMARK 500 GLN B 385 -65.85 -140.53 REMARK 500 ASN B 386 96.55 87.39 REMARK 500 LEU A 103 -87.76 -147.38 REMARK 500 ARG A 114 -49.28 70.99 REMARK 500 ASP A 158 147.03 97.22 REMARK 500 ASP A 360 133.97 176.34 REMARK 500 ASN A 379 40.48 -105.27 REMARK 500 GLN A 385 -62.79 -141.18 REMARK 500 ASN A 386 97.73 85.52 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 ASN A 359 ASP A 360 -149.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VDM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE WHICH REMARK 900 CATALYZES NON-GLYCOSIDIC C-N COUPLING IN VALIDAMYCIN A BIOSYNTHESIS REMARK 900 RELATED ID: 3VDN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN REMARK 900 COMPLEX WITH GDP, 2.55 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 4F97 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN REMARK 900 COMPLEX WITH GDP AND VALIDOXYLAMINE A 7'-PHOSPHATE REMARK 900 RELATED ID: 4F9F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VLDE, THE PSEUDO-GLYCOSYLTRANSFERASE, IN REMARK 900 COMPLEX WITH GDP AND TREHALOSE DBREF 4F96 B 1 497 UNP Q15JG1 Q15JG1_STRHY 1 497 DBREF 4F96 A 1 497 UNP Q15JG1 Q15JG1_STRHY 1 497 SEQRES 1 B 497 MET THR GLY SER GLU ILE PHE LEU ALA SER LYS ARG ALA SEQRES 2 B 497 ALA ILE THR TYR ASP THR ASP PRO ALA THR GLY GLU PRO SEQRES 3 B 497 ARG ALA TRP LEU ALA PRO GLY GLY THR GLY ASN VAL VAL SEQRES 4 B 497 ALA GLU GLN ALA GLY VAL LEU ASN ILE SER TRP ILE ALA SEQRES 5 B 497 SER ALA ASP SER GLU ASP ASP ARG ARG ALA SER ALA LEU SEQRES 6 B 497 ASN PRO ASP GLY VAL THR MET GLU LEU HIS SER GLY ARG SEQRES 7 B 497 GLU ILE LEU VAL ARG LEU ILE ARG HIS ASP PRO ALA VAL SEQRES 8 B 497 PHE ARG ASN VAL GLN ASN PHE MET THR ALA ASN LEU MET SEQRES 9 B 497 TRP ALA ALA ASN ASN TYR GLY TRP ASP ARG TRP THR GLN SEQRES 10 B 497 PRO SER PHE GLY SER ASP ALA ARG GLU GLY TRP ALA ASP SEQRES 11 B 497 PHE GLY ARG PHE THR ARG ASP PHE ALA ASP ALA ILE LEU SEQRES 12 B 497 LYS SER SER ALA GLN SER ALA ASP PRO VAL TYR LEU VAL SEQRES 13 B 497 HIS ASP TYR GLN LEU VAL GLY VAL PRO ALA LEU LEU ARG SEQRES 14 B 497 GLU GLN ARG PRO ASP ALA PRO ILE LEU LEU PHE VAL HIS SEQRES 15 B 497 ILE PRO TRP PRO SER ALA ASP TYR TRP ARG ILE LEU PRO SEQRES 16 B 497 LYS GLU ILE ARG THR GLY ILE LEU HIS GLY MET LEU PRO SEQRES 17 B 497 ALA THR THR ILE GLY PHE PHE ALA ASP ARG TRP CYS ARG SEQRES 18 B 497 ASN PHE LEU GLU SER VAL ALA ASP LEU LEU PRO ASP ALA SEQRES 19 B 497 ARG ILE ASP ARG GLU ALA MET THR VAL GLU TRP ARG GLY SEQRES 20 B 497 HIS ARG THR ARG LEU ARG THR MET PRO LEU GLY TYR SER SEQRES 21 B 497 PRO LEU THR LEU ASP GLY ARG ASN PRO GLN LEU PRO GLU SEQRES 22 B 497 GLY ILE GLU GLU TRP ALA ASP GLY HIS ARG LEU VAL VAL SEQRES 23 B 497 HIS SER GLY ARG THR ASP PRO ILE LYS ASN ALA GLU ARG SEQRES 24 B 497 ALA VAL ARG ALA PHE VAL LEU ALA ALA ARG GLY GLY GLY SEQRES 25 B 497 LEU GLU LYS THR ARG MET LEU VAL ARG MET ASN PRO ASN SEQRES 26 B 497 ARG LEU TYR VAL PRO ALA ASN ALA ASP TYR VAL HIS ARG SEQRES 27 B 497 VAL GLU THR ALA VAL ALA GLU ALA ASN ALA GLU LEU GLY SEQRES 28 B 497 SER ASP THR VAL ARG ILE ASP ASN ASP ASN ASP VAL ASN SEQRES 29 B 497 HIS THR ILE ALA CYS PHE ARG ARG ALA ASP LEU LEU ILE SEQRES 30 B 497 PHE ASN SER THR VAL ASP GLY GLN ASN LEU SER THR PHE SEQRES 31 B 497 GLU ALA PRO LEU VAL ASN GLU ARG ASP ALA ASP VAL ILE SEQRES 32 B 497 LEU SER GLU THR CYS GLY ALA ALA GLU VAL LEU GLY GLU SEQRES 33 B 497 TYR CYS ARG SER VAL ASN PRO PHE ASP LEU VAL GLU GLN SEQRES 34 B 497 ALA GLU ALA ILE SER ALA ALA LEU ALA ALA GLY PRO ARG SEQRES 35 B 497 GLN ARG ALA GLU ALA ALA ALA ARG ARG ARG ASP ALA ALA SEQRES 36 B 497 ARG PRO TRP THR LEU GLU ALA TRP VAL GLN ALA GLN LEU SEQRES 37 B 497 ASP GLY LEU ALA ALA ASP HIS ALA ALA ARG THR ALA THR SEQRES 38 B 497 ALA GLU ARG PHE ASP THR ALA PRO ALA VAL SER THR ARG SEQRES 39 B 497 ALA ASP LEU SEQRES 1 A 497 MET THR GLY SER GLU ILE PHE LEU ALA SER LYS ARG ALA SEQRES 2 A 497 ALA ILE THR TYR ASP THR ASP PRO ALA THR GLY GLU PRO SEQRES 3 A 497 ARG ALA TRP LEU ALA PRO GLY GLY THR GLY ASN VAL VAL SEQRES 4 A 497 ALA GLU GLN ALA GLY VAL LEU ASN ILE SER TRP ILE ALA SEQRES 5 A 497 SER ALA ASP SER GLU ASP ASP ARG ARG ALA SER ALA LEU SEQRES 6 A 497 ASN PRO ASP GLY VAL THR MET GLU LEU HIS SER GLY ARG SEQRES 7 A 497 GLU ILE LEU VAL ARG LEU ILE ARG HIS ASP PRO ALA VAL SEQRES 8 A 497 PHE ARG ASN VAL GLN ASN PHE MET THR ALA ASN LEU MET SEQRES 9 A 497 TRP ALA ALA ASN ASN TYR GLY TRP ASP ARG TRP THR GLN SEQRES 10 A 497 PRO SER PHE GLY SER ASP ALA ARG GLU GLY TRP ALA ASP SEQRES 11 A 497 PHE GLY ARG PHE THR ARG ASP PHE ALA ASP ALA ILE LEU SEQRES 12 A 497 LYS SER SER ALA GLN SER ALA ASP PRO VAL TYR LEU VAL SEQRES 13 A 497 HIS ASP TYR GLN LEU VAL GLY VAL PRO ALA LEU LEU ARG SEQRES 14 A 497 GLU GLN ARG PRO ASP ALA PRO ILE LEU LEU PHE VAL HIS SEQRES 15 A 497 ILE PRO TRP PRO SER ALA ASP TYR TRP ARG ILE LEU PRO SEQRES 16 A 497 LYS GLU ILE ARG THR GLY ILE LEU HIS GLY MET LEU PRO SEQRES 17 A 497 ALA THR THR ILE GLY PHE PHE ALA ASP ARG TRP CYS ARG SEQRES 18 A 497 ASN PHE LEU GLU SER VAL ALA ASP LEU LEU PRO ASP ALA SEQRES 19 A 497 ARG ILE ASP ARG GLU ALA MET THR VAL GLU TRP ARG GLY SEQRES 20 A 497 HIS ARG THR ARG LEU ARG THR MET PRO LEU GLY TYR SER SEQRES 21 A 497 PRO LEU THR LEU ASP GLY ARG ASN PRO GLN LEU PRO GLU SEQRES 22 A 497 GLY ILE GLU GLU TRP ALA ASP GLY HIS ARG LEU VAL VAL SEQRES 23 A 497 HIS SER GLY ARG THR ASP PRO ILE LYS ASN ALA GLU ARG SEQRES 24 A 497 ALA VAL ARG ALA PHE VAL LEU ALA ALA ARG GLY GLY GLY SEQRES 25 A 497 LEU GLU LYS THR ARG MET LEU VAL ARG MET ASN PRO ASN SEQRES 26 A 497 ARG LEU TYR VAL PRO ALA ASN ALA ASP TYR VAL HIS ARG SEQRES 27 A 497 VAL GLU THR ALA VAL ALA GLU ALA ASN ALA GLU LEU GLY SEQRES 28 A 497 SER ASP THR VAL ARG ILE ASP ASN ASP ASN ASP VAL ASN SEQRES 29 A 497 HIS THR ILE ALA CYS PHE ARG ARG ALA ASP LEU LEU ILE SEQRES 30 A 497 PHE ASN SER THR VAL ASP GLY GLN ASN LEU SER THR PHE SEQRES 31 A 497 GLU ALA PRO LEU VAL ASN GLU ARG ASP ALA ASP VAL ILE SEQRES 32 A 497 LEU SER GLU THR CYS GLY ALA ALA GLU VAL LEU GLY GLU SEQRES 33 A 497 TYR CYS ARG SER VAL ASN PRO PHE ASP LEU VAL GLU GLN SEQRES 34 A 497 ALA GLU ALA ILE SER ALA ALA LEU ALA ALA GLY PRO ARG SEQRES 35 A 497 GLN ARG ALA GLU ALA ALA ALA ARG ARG ARG ASP ALA ALA SEQRES 36 A 497 ARG PRO TRP THR LEU GLU ALA TRP VAL GLN ALA GLN LEU SEQRES 37 A 497 ASP GLY LEU ALA ALA ASP HIS ALA ALA ARG THR ALA THR SEQRES 38 A 497 ALA GLU ARG PHE ASP THR ALA PRO ALA VAL SER THR ARG SEQRES 39 A 497 ALA ASP LEU HET GDP B 501 28 HET CL B 502 1 HET GDP A 501 28 HET CL A 502 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM CL CHLORIDE ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 CL 2(CL 1-) FORMUL 7 HOH *405(H2 O) HELIX 1 1 GLY B 34 GLN B 42 1 9 HELIX 2 2 SER B 56 ASN B 66 1 11 HELIX 3 3 HIS B 75 GLY B 77 5 3 HELIX 4 4 ASP B 88 THR B 100 1 13 HELIX 5 5 LEU B 103 ASN B 109 1 7 HELIX 6 6 GLY B 121 SER B 146 1 26 HELIX 7 7 TYR B 159 VAL B 162 5 4 HELIX 8 8 GLY B 163 ARG B 172 1 10 HELIX 9 9 SER B 187 ARG B 192 1 6 HELIX 10 10 PRO B 195 LEU B 207 1 13 HELIX 11 11 ALA B 216 LEU B 231 1 16 HELIX 12 12 GLY B 274 ASP B 280 1 7 HELIX 13 13 ASP B 292 LYS B 295 5 4 HELIX 14 14 ASN B 296 GLY B 310 1 15 HELIX 15 15 VAL B 329 GLY B 351 1 23 HELIX 16 16 ASP B 362 ALA B 373 1 12 HELIX 17 17 LEU B 387 ASN B 396 1 10 HELIX 18 18 ALA B 410 GLY B 415 1 6 HELIX 19 19 GLU B 416 CYS B 418 5 3 HELIX 20 20 ASP B 425 ALA B 439 1 15 HELIX 21 21 GLY B 440 ARG B 456 1 17 HELIX 22 22 THR B 459 THR B 481 1 23 HELIX 23 23 GLY A 34 GLU A 41 1 8 HELIX 24 24 SER A 56 ASN A 66 1 11 HELIX 25 25 HIS A 75 GLY A 77 5 3 HELIX 26 26 ASP A 88 MET A 99 1 12 HELIX 27 27 LEU A 103 ASN A 109 1 7 HELIX 28 28 GLY A 121 SER A 146 1 26 HELIX 29 29 TYR A 159 VAL A 162 5 4 HELIX 30 30 GLY A 163 ARG A 172 1 10 HELIX 31 31 SER A 187 ARG A 192 1 6 HELIX 32 32 PRO A 195 LEU A 207 1 13 HELIX 33 33 ALA A 216 LEU A 231 1 16 HELIX 34 34 GLY A 274 ASP A 280 1 7 HELIX 35 35 ASP A 292 LYS A 295 5 4 HELIX 36 36 ASN A 296 GLY A 310 1 15 HELIX 37 37 VAL A 329 GLY A 351 1 23 HELIX 38 38 ASP A 362 ALA A 373 1 12 HELIX 39 39 LEU A 387 ASN A 396 1 10 HELIX 40 40 ALA A 410 GLY A 415 1 6 HELIX 41 41 GLU A 416 CYS A 418 5 3 HELIX 42 42 ASP A 425 ALA A 439 1 15 HELIX 43 43 GLY A 440 ARG A 456 1 17 HELIX 44 44 THR A 459 THR A 481 1 23 SHEET 1 A10 VAL B 70 GLU B 73 0 SHEET 2 A10 GLU B 79 ILE B 85 -1 O ILE B 80 N MET B 72 SHEET 3 A10 ASN B 47 SER B 53 1 N TRP B 50 O LEU B 81 SHEET 4 A10 GLU B 5 ALA B 9 1 N LEU B 8 O ILE B 51 SHEET 5 A10 PRO B 152 HIS B 157 1 O VAL B 153 N PHE B 7 SHEET 6 A10 ILE B 177 PHE B 180 1 O LEU B 178 N VAL B 156 SHEET 7 A10 THR B 211 PHE B 214 1 O GLY B 213 N LEU B 179 SHEET 8 A10 HIS B 248 THR B 254 1 O ARG B 253 N ILE B 212 SHEET 9 A10 THR B 242 TRP B 245 -1 N VAL B 243 O THR B 250 SHEET 10 A10 ARG B 235 ASP B 237 -1 N ARG B 235 O GLU B 244 SHEET 1 B 2 ILE B 15 THR B 19 0 SHEET 2 B 2 PRO B 26 LEU B 30 -1 O TRP B 29 N THR B 16 SHEET 1 C 6 VAL B 355 ASN B 359 0 SHEET 2 C 6 THR B 316 ASN B 323 1 N VAL B 320 O ARG B 356 SHEET 3 C 6 ARG B 283 ARG B 290 1 N VAL B 285 O LEU B 319 SHEET 4 C 6 LEU B 375 PHE B 378 1 O LEU B 375 N VAL B 286 SHEET 5 C 6 ASP B 401 SER B 405 1 O ILE B 403 N LEU B 376 SHEET 6 C 6 ARG B 419 VAL B 421 1 O ARG B 419 N VAL B 402 SHEET 1 D10 VAL A 70 GLU A 73 0 SHEET 2 D10 GLU A 79 ILE A 85 -1 O VAL A 82 N VAL A 70 SHEET 3 D10 ASN A 47 SER A 53 1 N TRP A 50 O ARG A 83 SHEET 4 D10 GLU A 5 ALA A 9 1 N LEU A 8 O ILE A 51 SHEET 5 D10 PRO A 152 HIS A 157 1 O VAL A 153 N PHE A 7 SHEET 6 D10 ILE A 177 PHE A 180 1 O LEU A 178 N VAL A 156 SHEET 7 D10 THR A 211 PHE A 214 1 O GLY A 213 N LEU A 179 SHEET 8 D10 HIS A 248 THR A 254 1 O ARG A 253 N ILE A 212 SHEET 9 D10 THR A 242 TRP A 245 -1 N TRP A 245 O HIS A 248 SHEET 10 D10 ARG A 235 ASP A 237 -1 N ARG A 235 O GLU A 244 SHEET 1 E 2 ILE A 15 THR A 19 0 SHEET 2 E 2 PRO A 26 LEU A 30 -1 O ARG A 27 N ASP A 18 SHEET 1 F 6 VAL A 355 ASN A 359 0 SHEET 2 F 6 THR A 316 ASN A 323 1 N VAL A 320 O ARG A 356 SHEET 3 F 6 ARG A 283 ARG A 290 1 N VAL A 285 O LEU A 319 SHEET 4 F 6 LEU A 375 PHE A 378 1 O LEU A 375 N VAL A 286 SHEET 5 F 6 ASP A 401 SER A 405 1 O ILE A 403 N PHE A 378 SHEET 6 F 6 ARG A 419 VAL A 421 1 O ARG A 419 N VAL A 402 CISPEP 1 GLN B 117 PRO B 118 0 -3.29 CISPEP 2 GLN A 117 PRO A 118 0 -3.34 SITE 1 AC1 19 ARG B 290 LYS B 295 ARG B 321 ASN B 323 SITE 2 AC1 19 ASP B 360 ASN B 361 ASP B 362 THR B 366 SITE 3 AC1 19 ASN B 386 LEU B 387 SER B 388 GLU B 391 SITE 4 AC1 19 HOH B 660 HOH B 675 HOH B 676 HOH B 688 SITE 5 AC1 19 HOH B 706 HOH B 716 HOH B 779 SITE 1 AC2 4 ARG A 114 CL A 502 TYR B 110 SER B 187 SITE 1 AC3 18 ARG A 290 LYS A 295 ARG A 321 ASN A 323 SITE 2 AC3 18 ASP A 360 ASN A 361 ASP A 362 VAL A 363 SITE 3 AC3 18 THR A 366 ASN A 386 LEU A 387 SER A 388 SITE 4 AC3 18 GLU A 391 HOH A 663 HOH A 677 HOH A 687 SITE 5 AC3 18 HOH A 695 HOH A 722 SITE 1 AC4 4 TYR A 110 SER A 187 ARG B 114 CL B 502 CRYST1 47.821 121.151 84.333 90.00 91.74 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 0.020911 0.000000 0.000634 0.00000 SCALE2 0.000000 0.008254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011863 0.00000