HEADER TRANSFERASE 07-SEP-16 5GVV TITLE CRYSTAL STRUCTURE OF THE GLYCOSYLTRANSFERASE GLYE IN STREPTOCOCCUS TITLE 2 PNEUMONIAE TIGR4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYL TRANSFERASE FAMILY 8; COMPND 3 CHAIN: A, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: GSPA_4, ERS409372_01175, ERS515225_01083; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS THE GLYCOSYLTRANSFERASE, SERINE-RICH REPEAT PROTEIN, STREPTOCOCCUS KEYWDS 2 PNEUMONIAE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.JIANG,H.JIN,R.L.ZHAO,H.B.YANG,Y.CHEN,C.Z.ZHOU REVDAT 3 06-DEC-17 5GVV 1 JRNL REVDAT 2 18-OCT-17 5GVV 1 REMARK REVDAT 1 01-MAR-17 5GVV 0 JRNL AUTH Y.L.JIANG,H.JIN,H.B.YANG,R.L.ZHAO,S.WANG,Y.CHEN,C.Z.ZHOU JRNL TITL DEFINING THE ENZYMATIC PATHWAY FOR POLYMORPHIC JRNL TITL 2 O-GLYCOSYLATION OF THE PNEUMOCOCCAL SERINE-RICH REPEAT JRNL TITL 3 PROTEIN PSRP. JRNL REF J. BIOL. CHEM. V. 292 6213 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28246170 JRNL DOI 10.1074/JBC.M116.770446 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 61260 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 3105 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 48.8250 - 5.4616 1.00 2930 144 0.2015 0.2163 REMARK 3 2 5.4616 - 4.3358 0.98 2763 126 0.1661 0.1876 REMARK 3 3 4.3358 - 3.7880 1.00 2760 139 0.1717 0.2005 REMARK 3 4 3.7880 - 3.4418 1.00 2742 144 0.1803 0.2438 REMARK 3 5 3.4418 - 3.1951 1.00 2738 140 0.1847 0.2476 REMARK 3 6 3.1951 - 3.0068 1.00 2711 144 0.1980 0.2448 REMARK 3 7 3.0068 - 2.8562 0.99 2671 162 0.1929 0.2517 REMARK 3 8 2.8562 - 2.7319 0.99 2716 132 0.1995 0.2468 REMARK 3 9 2.7319 - 2.6267 0.99 2677 132 0.2040 0.2793 REMARK 3 10 2.6267 - 2.5361 0.98 2655 152 0.2008 0.2789 REMARK 3 11 2.5361 - 2.4568 0.99 2660 130 0.1942 0.2588 REMARK 3 12 2.4568 - 2.3866 0.99 2667 149 0.2048 0.2965 REMARK 3 13 2.3866 - 2.3237 0.98 2604 137 0.2075 0.2833 REMARK 3 14 2.3237 - 2.2671 0.98 2654 135 0.2218 0.2733 REMARK 3 15 2.2671 - 2.2155 0.96 2574 125 0.3269 0.3772 REMARK 3 16 2.2155 - 2.1684 0.96 2577 154 0.2117 0.2677 REMARK 3 17 2.1684 - 2.1250 0.96 2575 144 0.2229 0.2811 REMARK 3 18 2.1250 - 2.0849 0.94 2485 171 0.2259 0.3214 REMARK 3 19 2.0849 - 2.0477 0.94 2510 147 0.2859 0.3802 REMARK 3 20 2.0477 - 2.0129 0.94 2459 164 0.2360 0.2776 REMARK 3 21 2.0129 - 1.9805 0.94 2519 125 0.2457 0.3049 REMARK 3 22 1.9805 - 1.9500 0.92 2508 109 0.2556 0.2991 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.190 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 6602 REMARK 3 ANGLE : 0.942 8958 REMARK 3 CHIRALITY : 0.064 971 REMARK 3 PLANARITY : 0.004 1129 REMARK 3 DIHEDRAL : 15.250 2422 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5GVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1300001559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL 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 : 61392 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 48.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 45.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M HEPES, PH 7.5, 25% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 37.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.18000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.18000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.10500 REMARK 290 SMTRY3 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 MSE A 1 REMARK 465 ARG A 2 REMARK 465 GLN A 73 REMARK 465 MSE A 74 REMARK 465 ASN A 75 REMARK 465 TRP A 76 REMARK 465 SER A 77 REMARK 465 ASN A 78 REMARK 465 LYS A 79 REMARK 465 LEU A 80 REMARK 465 PRO A 81 REMARK 465 HIS A 82 REMARK 465 ILE A 83 REMARK 465 ASN A 84 REMARK 465 MSE F 1 REMARK 465 ARG F 2 REMARK 465 ASN F 3 REMARK 465 THR F 4 REMARK 465 GLN F 73 REMARK 465 MSE F 74 REMARK 465 ASN F 75 REMARK 465 TRP F 76 REMARK 465 SER F 77 REMARK 465 ASN F 78 REMARK 465 LYS F 79 REMARK 465 LEU F 80 REMARK 465 PRO F 81 REMARK 465 HIS F 82 REMARK 465 ILE F 83 REMARK 465 ASN F 84 REMARK 465 HIS F 85 REMARK 465 SER F 381 REMARK 465 GLU F 382 REMARK 465 ILE F 383 REMARK 465 SER F 384 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 F 830 O HOH F 840 2.17 REMARK 500 OE2 GLU F 193 O HOH F 601 2.17 REMARK 500 O HOH A 700 O HOH A 837 2.17 REMARK 500 O HOH A 708 O HOH A 825 2.18 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 MSE A 86 N - CA - C ANGL. DEV. = 21.8 DEGREES REMARK 500 MSE F 86 CB - CA - C ANGL. DEV. = -14.8 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 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 MSE A 86 -85.95 -60.53 REMARK 500 ASP A 108 44.01 -94.10 REMARK 500 PHE A 135 14.51 58.99 REMARK 500 ASN A 197 70.48 -163.58 REMARK 500 SER A 230 -178.39 78.43 REMARK 500 GLN F 71 8.92 -69.90 REMARK 500 THR F 87 4.17 26.33 REMARK 500 ASP F 108 43.42 -95.48 REMARK 500 GLU F 169 -7.78 60.91 REMARK 500 ASN F 197 64.20 -164.12 REMARK 500 SER F 230 176.12 81.77 REMARK 500 ASP F 352 -143.91 62.74 REMARK 500 GLU F 378 44.52 -89.81 REMARK 500 ASN F 379 26.16 -158.87 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 872 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH F 881 DISTANCE = 5.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 106 OD2 REMARK 620 2 ASP A 108 OD1 104.9 REMARK 620 3 ASP A 108 OD2 162.5 60.9 REMARK 620 4 HIS A 227 NE2 94.3 91.3 96.1 REMARK 620 5 UDP A 502 O1A 93.7 86.5 76.1 172.0 REMARK 620 6 UDP A 502 O3B 96.6 157.4 96.7 94.0 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN F 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 106 OD2 REMARK 620 2 ASP F 108 OD1 103.2 REMARK 620 3 ASP F 108 OD2 160.0 60.7 REMARK 620 4 HIS F 227 NE2 96.4 94.2 96.6 REMARK 620 5 UDP F 502 O2A 90.4 85.1 77.1 173.1 REMARK 620 6 UDP F 502 O2B 97.4 155.7 96.2 96.1 82.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN F 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP F 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GVW RELATED DB: PDB DBREF1 5GVV A 1 406 UNP A0A0Y1PI62_STREE DBREF2 5GVV A A0A0Y1PI62 1 406 DBREF1 5GVV F 1 406 UNP A0A0Y1PI62_STREE DBREF2 5GVV F A0A0Y1PI62 1 406 SEQRES 1 A 406 MSE ARG ASN THR LYS ARG ALA VAL VAL PHE ALA GLY ASP SEQRES 2 A 406 TYR ALA TYR ILE ARG GLN ILE GLU THR ALA MSE LYS SER SEQRES 3 A 406 LEU CYS ARG HIS ASN SER HIS LEU LYS ILE TYR LEU LEU SEQRES 4 A 406 ASN GLN ASP ILE PRO GLN GLU TRP PHE SER GLN ILE ARG SEQRES 5 A 406 ILE TYR LEU GLN GLU MSE GLY GLY ASP LEU ILE ASP CYS SEQRES 6 A 406 LYS LEU ILE GLY SER GLN PHE GLN MSE ASN TRP SER ASN SEQRES 7 A 406 LYS LEU PRO HIS ILE ASN HIS MSE THR PHE ALA ARG TYR SEQRES 8 A 406 PHE ILE PRO ASP PHE VAL THR GLU ASP LYS VAL LEU TYR SEQRES 9 A 406 LEU ASP SER ASP LEU ILE VAL THR GLY ASP LEU THR ASP SEQRES 10 A 406 LEU PHE GLU LEU ASP LEU GLY GLU ASN TYR LEU ALA ALA SEQRES 11 A 406 ALA ARG SER CYS PHE GLY ALA GLY VAL GLY PHE ASN ALA SEQRES 12 A 406 GLY VAL LEU LEU ILE ASN ASN LYS LYS TRP GLY SER GLU SEQRES 13 A 406 THR ILE ARG GLN LYS LEU ILE ASP LEU THR GLU LYS GLU SEQRES 14 A 406 HIS GLU ASN VAL GLU GLU GLY ASP GLN SER ILE LEU ASN SEQRES 15 A 406 MSE LEU PHE LYS ASP GLN TYR SER SER LEU GLU ASP GLN SEQRES 16 A 406 TYR ASN PHE GLN ILE GLY TYR ASP TYR GLY ALA ALA THR SEQRES 17 A 406 PHE LYS HIS GLN PHE ILE PHE ASP ILE PRO LEU GLU PRO SEQRES 18 A 406 LEU PRO LEU ILE LEU HIS TYR ILE SER GLN ASP LYS PRO SEQRES 19 A 406 TRP ASN GLN PHE SER VAL GLY ARG LEU ARG GLU VAL TRP SEQRES 20 A 406 TRP GLU TYR SER LEU MSE ASP TRP SER VAL ILE LEU ASN SEQRES 21 A 406 GLU TRP PHE SER LYS SER VAL LYS TYR PRO SER LYS SER SEQRES 22 A 406 GLN ILE PHE LYS LEU GLN CYS VAL ASN LEU THR ASN SER SEQRES 23 A 406 TRP CYS VAL GLU LYS ILE ASP TYR LEU ALA GLU GLN LEU SEQRES 24 A 406 PRO GLU VAL HIS PHE HIS ILE VAL ALA TYR THR ASN MSE SEQRES 25 A 406 ALA ASN GLU LEU LEU ALA LEU THR ARG PHE PRO ASN VAL SEQRES 26 A 406 THR VAL TYR PRO ASN SER LEU PRO MSE LEU LEU GLU GLN SEQRES 27 A 406 ILE VAL ILE ALA SER ASP LEU TYR LEU ASP LEU ASN HIS SEQRES 28 A 406 ASP ARG LYS LEU GLU ASP ALA TYR GLU PHE VAL LEU LYS SEQRES 29 A 406 TYR LYS LYS PRO MSE ILE ALA PHE ASP ASN THR CYS SER SEQRES 30 A 406 GLU ASN LEU SER GLU ILE SER TYR GLU GLY ILE TYR PRO SEQRES 31 A 406 SER SER ILE PRO LYS LYS MSE VAL ALA ALA ILE ARG SER SEQRES 32 A 406 TYR MSE ARG SEQRES 1 F 406 MSE ARG ASN THR LYS ARG ALA VAL VAL PHE ALA GLY ASP SEQRES 2 F 406 TYR ALA TYR ILE ARG GLN ILE GLU THR ALA MSE LYS SER SEQRES 3 F 406 LEU CYS ARG HIS ASN SER HIS LEU LYS ILE TYR LEU LEU SEQRES 4 F 406 ASN GLN ASP ILE PRO GLN GLU TRP PHE SER GLN ILE ARG SEQRES 5 F 406 ILE TYR LEU GLN GLU MSE GLY GLY ASP LEU ILE ASP CYS SEQRES 6 F 406 LYS LEU ILE GLY SER GLN PHE GLN MSE ASN TRP SER ASN SEQRES 7 F 406 LYS LEU PRO HIS ILE ASN HIS MSE THR PHE ALA ARG TYR SEQRES 8 F 406 PHE ILE PRO ASP PHE VAL THR GLU ASP LYS VAL LEU TYR SEQRES 9 F 406 LEU ASP SER ASP LEU ILE VAL THR GLY ASP LEU THR ASP SEQRES 10 F 406 LEU PHE GLU LEU ASP LEU GLY GLU ASN TYR LEU ALA ALA SEQRES 11 F 406 ALA ARG SER CYS PHE GLY ALA GLY VAL GLY PHE ASN ALA SEQRES 12 F 406 GLY VAL LEU LEU ILE ASN ASN LYS LYS TRP GLY SER GLU SEQRES 13 F 406 THR ILE ARG GLN LYS LEU ILE ASP LEU THR GLU LYS GLU SEQRES 14 F 406 HIS GLU ASN VAL GLU GLU GLY ASP GLN SER ILE LEU ASN SEQRES 15 F 406 MSE LEU PHE LYS ASP GLN TYR SER SER LEU GLU ASP GLN SEQRES 16 F 406 TYR ASN PHE GLN ILE GLY TYR ASP TYR GLY ALA ALA THR SEQRES 17 F 406 PHE LYS HIS GLN PHE ILE PHE ASP ILE PRO LEU GLU PRO SEQRES 18 F 406 LEU PRO LEU ILE LEU HIS TYR ILE SER GLN ASP LYS PRO SEQRES 19 F 406 TRP ASN GLN PHE SER VAL GLY ARG LEU ARG GLU VAL TRP SEQRES 20 F 406 TRP GLU TYR SER LEU MSE ASP TRP SER VAL ILE LEU ASN SEQRES 21 F 406 GLU TRP PHE SER LYS SER VAL LYS TYR PRO SER LYS SER SEQRES 22 F 406 GLN ILE PHE LYS LEU GLN CYS VAL ASN LEU THR ASN SER SEQRES 23 F 406 TRP CYS VAL GLU LYS ILE ASP TYR LEU ALA GLU GLN LEU SEQRES 24 F 406 PRO GLU VAL HIS PHE HIS ILE VAL ALA TYR THR ASN MSE SEQRES 25 F 406 ALA ASN GLU LEU LEU ALA LEU THR ARG PHE PRO ASN VAL SEQRES 26 F 406 THR VAL TYR PRO ASN SER LEU PRO MSE LEU LEU GLU GLN SEQRES 27 F 406 ILE VAL ILE ALA SER ASP LEU TYR LEU ASP LEU ASN HIS SEQRES 28 F 406 ASP ARG LYS LEU GLU ASP ALA TYR GLU PHE VAL LEU LYS SEQRES 29 F 406 TYR LYS LYS PRO MSE ILE ALA PHE ASP ASN THR CYS SER SEQRES 30 F 406 GLU ASN LEU SER GLU ILE SER TYR GLU GLY ILE TYR PRO SEQRES 31 F 406 SER SER ILE PRO LYS LYS MSE VAL ALA ALA ILE ARG SER SEQRES 32 F 406 TYR MSE ARG MODRES 5GVV MSE A 24 MET MODIFIED RESIDUE MODRES 5GVV MSE A 58 MET MODIFIED RESIDUE MODRES 5GVV MSE A 86 MET MODIFIED RESIDUE MODRES 5GVV MSE A 183 MET MODIFIED RESIDUE MODRES 5GVV MSE A 253 MET MODIFIED RESIDUE MODRES 5GVV MSE A 312 MET MODIFIED RESIDUE MODRES 5GVV MSE A 334 MET MODIFIED RESIDUE MODRES 5GVV MSE A 369 MET MODIFIED RESIDUE MODRES 5GVV MSE A 397 MET MODIFIED RESIDUE MODRES 5GVV MSE A 405 MET MODIFIED RESIDUE MODRES 5GVV MSE F 24 MET MODIFIED RESIDUE MODRES 5GVV MSE F 58 MET MODIFIED RESIDUE MODRES 5GVV MSE F 86 MET MODIFIED RESIDUE MODRES 5GVV MSE F 183 MET MODIFIED RESIDUE MODRES 5GVV MSE F 253 MET MODIFIED RESIDUE MODRES 5GVV MSE F 312 MET MODIFIED RESIDUE MODRES 5GVV MSE F 334 MET MODIFIED RESIDUE MODRES 5GVV MSE F 369 MET MODIFIED RESIDUE MODRES 5GVV MSE F 397 MET MODIFIED RESIDUE MODRES 5GVV MSE F 405 MET MODIFIED RESIDUE HET MSE A 24 8 HET MSE A 58 8 HET MSE A 86 8 HET MSE A 183 8 HET MSE A 253 8 HET MSE A 312 8 HET MSE A 334 8 HET MSE A 369 8 HET MSE A 397 8 HET MSE A 405 8 HET MSE F 24 8 HET MSE F 58 8 HET MSE F 86 8 HET MSE F 183 8 HET MSE F 253 8 HET MSE F 312 8 HET MSE F 334 8 HET MSE F 369 8 HET MSE F 397 8 HET MSE F 405 8 HET MN A 501 1 HET UDP A 502 25 HET MN F 501 1 HET UDP F 502 25 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE FORMUL 1 MSE 20(C5 H11 N O2 SE) FORMUL 3 MN 2(MN 2+) FORMUL 4 UDP 2(C9 H14 N2 O12 P2) FORMUL 7 HOH *553(H2 O) HELIX 1 AA1 ASP A 13 ALA A 15 5 3 HELIX 2 AA2 TYR A 16 ASN A 31 1 16 HELIX 3 AA3 PRO A 44 MSE A 58 1 15 HELIX 4 AA4 PHE A 88 PHE A 96 5 9 HELIX 5 AA5 LEU A 115 GLU A 120 1 6 HELIX 6 AA6 SER A 133 ALA A 137 5 5 HELIX 7 AA7 ASN A 150 GLU A 156 1 7 HELIX 8 AA8 THR A 157 LYS A 168 1 12 HELIX 9 AA9 GLU A 175 LYS A 186 1 12 HELIX 10 AB1 GLU A 193 ASN A 197 5 5 HELIX 11 AB2 GLN A 199 GLY A 201 5 3 HELIX 12 AB3 TYR A 202 PHE A 209 1 8 HELIX 13 AB4 HIS A 211 ILE A 217 5 7 HELIX 14 AB5 LEU A 243 LEU A 252 1 10 HELIX 15 AB6 ASP A 254 SER A 264 1 11 HELIX 16 AB7 LYS A 291 LEU A 299 1 9 HELIX 17 AB8 ALA A 313 ALA A 318 1 6 HELIX 18 AB9 LEU A 319 PHE A 322 5 4 HELIX 19 AC1 LEU A 332 SER A 343 1 12 HELIX 20 AC2 LEU A 355 TYR A 365 1 11 HELIX 21 AC3 SER A 381 TYR A 385 5 5 HELIX 22 AC4 PRO A 394 SER A 403 1 10 HELIX 23 AC5 ASP F 13 ALA F 15 5 3 HELIX 24 AC6 TYR F 16 ASN F 31 1 16 HELIX 25 AC7 PRO F 44 MSE F 58 1 15 HELIX 26 AC8 PHE F 88 TYR F 91 5 4 HELIX 27 AC9 PHE F 92 VAL F 97 1 6 HELIX 28 AD1 LEU F 115 GLU F 120 1 6 HELIX 29 AD2 CYS F 134 ALA F 137 5 4 HELIX 30 AD3 ASN F 150 GLU F 156 1 7 HELIX 31 AD4 THR F 157 LYS F 168 1 12 HELIX 32 AD5 GLU F 175 LYS F 186 1 12 HELIX 33 AD6 GLU F 193 ASN F 197 5 5 HELIX 34 AD7 GLN F 199 GLY F 201 5 3 HELIX 35 AD8 TYR F 202 LYS F 210 1 9 HELIX 36 AD9 HIS F 211 ILE F 217 5 7 HELIX 37 AE1 LEU F 243 LEU F 252 1 10 HELIX 38 AE2 ASP F 254 SER F 264 1 11 HELIX 39 AE3 LYS F 291 LEU F 299 1 9 HELIX 40 AE4 ALA F 313 ALA F 318 1 6 HELIX 41 AE5 LEU F 319 PHE F 322 5 4 HELIX 42 AE6 LEU F 332 SER F 343 1 12 HELIX 43 AE7 LEU F 355 TYR F 365 1 11 HELIX 44 AE8 PRO F 394 ARG F 402 1 9 SHEET 1 AA1 7 ASP A 61 LYS A 66 0 SHEET 2 AA1 7 LEU A 34 ASN A 40 1 N ILE A 36 O ILE A 63 SHEET 3 AA1 7 ARG A 6 ALA A 11 1 N VAL A 8 O TYR A 37 SHEET 4 AA1 7 LYS A 101 LEU A 105 1 O LEU A 103 N VAL A 9 SHEET 5 AA1 7 VAL A 145 ASN A 149 -1 O ILE A 148 N VAL A 102 SHEET 6 AA1 7 LEU A 128 ALA A 131 -1 N ALA A 129 O LEU A 147 SHEET 7 AA1 7 TYR A 189 LEU A 192 1 O SER A 190 N LEU A 128 SHEET 1 AA2 2 LEU A 109 VAL A 111 0 SHEET 2 AA2 2 ILE A 225 HIS A 227 -1 O LEU A 226 N ILE A 110 SHEET 1 AA3 6 VAL A 325 TYR A 328 0 SHEET 2 AA3 6 VAL A 302 VAL A 307 1 N PHE A 304 O THR A 326 SHEET 3 AA3 6 LEU A 278 LEU A 283 1 N ASN A 282 O VAL A 307 SHEET 4 AA3 6 LEU A 345 ASP A 348 1 O LEU A 347 N VAL A 281 SHEET 5 AA3 6 MSE A 369 PHE A 372 1 O ILE A 370 N ASP A 348 SHEET 6 AA3 6 GLY A 387 TYR A 389 1 O TYR A 389 N ALA A 371 SHEET 1 AA4 7 ASP F 61 LYS F 66 0 SHEET 2 AA4 7 LEU F 34 ASN F 40 1 N ILE F 36 O ILE F 63 SHEET 3 AA4 7 ARG F 6 ALA F 11 1 N VAL F 8 O TYR F 37 SHEET 4 AA4 7 LYS F 101 LEU F 105 1 O LEU F 103 N VAL F 9 SHEET 5 AA4 7 PHE F 141 ASN F 149 -1 O LEU F 146 N TYR F 104 SHEET 6 AA4 7 LEU F 128 ARG F 132 -1 N ALA F 131 O ASN F 142 SHEET 7 AA4 7 TYR F 189 LEU F 192 1 O SER F 190 N LEU F 128 SHEET 1 AA5 2 LEU F 109 VAL F 111 0 SHEET 2 AA5 2 ILE F 225 HIS F 227 -1 O LEU F 226 N ILE F 110 SHEET 1 AA6 6 VAL F 325 TYR F 328 0 SHEET 2 AA6 6 VAL F 302 VAL F 307 1 N PHE F 304 O THR F 326 SHEET 3 AA6 6 LEU F 278 LEU F 283 1 N ASN F 282 O VAL F 307 SHEET 4 AA6 6 LEU F 345 ASP F 348 1 O LEU F 347 N VAL F 281 SHEET 5 AA6 6 MSE F 369 PHE F 372 1 O ILE F 370 N ASP F 348 SHEET 6 AA6 6 GLY F 387 TYR F 389 1 O TYR F 389 N ALA F 371 LINK C ALA A 23 N MSE A 24 1555 1555 1.34 LINK C MSE A 24 N LYS A 25 1555 1555 1.33 LINK C GLU A 57 N MSE A 58 1555 1555 1.30 LINK C MSE A 58 N GLY A 59 1555 1555 1.34 LINK C HIS A 85 N MSE A 86 1555 1555 1.31 LINK C MSE A 86 N THR A 87 1555 1555 1.31 LINK OD2 ASP A 106 MN MN A 501 1555 1555 2.07 LINK OD1 ASP A 108 MN MN A 501 1555 1555 2.10 LINK OD2 ASP A 108 MN MN A 501 1555 1555 2.24 LINK C ASN A 182 N MSE A 183 1555 1555 1.31 LINK C MSE A 183 N LEU A 184 1555 1555 1.32 LINK NE2 HIS A 227 MN MN A 501 1555 1555 2.12 LINK C LEU A 252 N MSE A 253 1555 1555 1.33 LINK C MSE A 253 N ASP A 254 1555 1555 1.33 LINK C ASN A 311 N MSE A 312 1555 1555 1.33 LINK C MSE A 312 N ALA A 313 1555 1555 1.33 LINK C PRO A 333 N MSE A 334 1555 1555 1.33 LINK C MSE A 334 N LEU A 335 1555 1555 1.31 LINK C PRO A 368 N MSE A 369 1555 1555 1.33 LINK C MSE A 369 N ILE A 370 1555 1555 1.33 LINK C LYS A 396 N MSE A 397 1555 1555 1.33 LINK C MSE A 397 N VAL A 398 1555 1555 1.33 LINK C TYR A 404 N MSE A 405 1555 1555 1.29 LINK C MSE A 405 N ARG A 406 1555 1555 1.32 LINK C ALA F 23 N MSE F 24 1555 1555 1.34 LINK C MSE F 24 N LYS F 25 1555 1555 1.34 LINK C GLU F 57 N MSE F 58 1555 1555 1.32 LINK C MSE F 58 N GLY F 59 1555 1555 1.34 LINK C MSE F 86 N THR F 87 1555 1555 1.35 LINK OD2 ASP F 106 MN MN F 501 1555 1555 2.14 LINK OD1 ASP F 108 MN MN F 501 1555 1555 2.12 LINK OD2 ASP F 108 MN MN F 501 1555 1555 2.20 LINK C ASN F 182 N MSE F 183 1555 1555 1.32 LINK C MSE F 183 N LEU F 184 1555 1555 1.31 LINK NE2 HIS F 227 MN MN F 501 1555 1555 2.12 LINK C LEU F 252 N MSE F 253 1555 1555 1.33 LINK C MSE F 253 N ASP F 254 1555 1555 1.33 LINK C ASN F 311 N MSE F 312 1555 1555 1.33 LINK C MSE F 312 N ALA F 313 1555 1555 1.33 LINK C PRO F 333 N MSE F 334 1555 1555 1.34 LINK C MSE F 334 N LEU F 335 1555 1555 1.33 LINK C PRO F 368 N MSE F 369 1555 1555 1.33 LINK C MSE F 369 N ILE F 370 1555 1555 1.33 LINK C LYS F 396 N MSE F 397 1555 1555 1.33 LINK C MSE F 397 N VAL F 398 1555 1555 1.33 LINK C TYR F 404 N MSE F 405 1555 1555 1.31 LINK C MSE F 405 N ARG F 406 1555 1555 1.33 LINK MN MN A 501 O1A UDP A 502 1555 1555 2.14 LINK MN MN A 501 O3B UDP A 502 1555 1555 2.02 LINK MN MN F 501 O2A UDP F 502 1555 1555 2.11 LINK MN MN F 501 O2B UDP F 502 1555 1555 1.97 CISPEP 1 HIS A 85 MSE A 86 0 9.03 CISPEP 2 GLU A 220 PRO A 221 0 -0.45 CISPEP 3 GLU F 220 PRO F 221 0 8.78 SITE 1 AC1 4 ASP A 106 ASP A 108 HIS A 227 UDP A 502 SITE 1 AC2 16 ALA A 11 GLY A 12 ASP A 13 TYR A 16 SITE 2 AC2 16 THR A 87 ARG A 90 ASP A 106 SER A 107 SITE 3 AC2 16 ASP A 108 HIS A 227 ILE A 229 SER A 230 SITE 4 AC2 16 LYS A 233 MN A 501 HOH A 616 HOH A 623 SITE 1 AC3 4 ASP F 106 ASP F 108 HIS F 227 UDP F 502 SITE 1 AC4 14 ALA F 11 GLY F 12 ASP F 13 TYR F 16 SITE 2 AC4 14 THR F 87 ASP F 106 SER F 107 ASP F 108 SITE 3 AC4 14 HIS F 227 ILE F 229 SER F 230 LYS F 233 SITE 4 AC4 14 MN F 501 HOH F 608 CRYST1 75.170 88.210 128.360 90.00 90.00 90.00 P 21 21 21 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 0.013303 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011337 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007791 0.00000