HEADER TRANSFERASE 07-JAN-17 5WXI TITLE EARP BOUND WITH DTDP-RHAMNOSE (SOAKED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: EARP; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS SEROGROUP B / SEROTYPE SOURCE 3 15 (STRAIN H44/76); SOURCE 4 ORGANISM_TAXID: 909420; SOURCE 5 STRAIN: H44/76; SOURCE 6 GENE: NMH_0797; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28C KEYWDS GLYCOSYLTRANSFERASE, GT-B, EF-P, RHAMNOSYLATION, TRANSLATION KEYWDS 2 ELONGATION, DTDP-RHAMNOSE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SENGOKU,S.YOKOYAMA,T.YANAGISAWA REVDAT 3 03-APR-24 5WXI 1 REMARK REVDAT 2 04-APR-18 5WXI 1 JRNL REVDAT 1 28-FEB-18 5WXI 0 JRNL AUTH T.SENGOKU,T.SUZUKI,N.DOHMAE,C.WATANABE,T.HONMA,Y.HIKIDA, JRNL AUTH 2 Y.YAMAGUCHI,H.TAKAHASHI,S.YOKOYAMA,T.YANAGISAWA JRNL TITL STRUCTURAL BASIS OF PROTEIN ARGININE RHAMNOSYLATION BY JRNL TITL 2 GLYCOSYLTRANSFERASE EARP JRNL REF NAT. CHEM. BIOL. V. 14 368 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 29440735 JRNL DOI 10.1038/S41589-018-0002-Y REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 60983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 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 48.8615 - 4.3082 1.00 6296 155 0.1598 0.1894 REMARK 3 2 4.3082 - 3.4198 1.00 6058 148 0.1437 0.1959 REMARK 3 3 3.4198 - 2.9876 1.00 5972 147 0.1621 0.1996 REMARK 3 4 2.9876 - 2.7144 1.00 5918 146 0.1761 0.2387 REMARK 3 5 2.7144 - 2.5199 1.00 5934 146 0.1781 0.2177 REMARK 3 6 2.5199 - 2.3713 1.00 5895 146 0.1860 0.2332 REMARK 3 7 2.3713 - 2.2526 1.00 5880 144 0.1871 0.2216 REMARK 3 8 2.2526 - 2.1545 1.00 5890 144 0.1964 0.2434 REMARK 3 9 2.1545 - 2.0716 1.00 5840 145 0.2167 0.2609 REMARK 3 10 2.0716 - 2.0001 1.00 5835 144 0.2369 0.2414 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.110 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 : 0.006 6525 REMARK 3 ANGLE : 0.850 8899 REMARK 3 CHIRALITY : 0.051 929 REMARK 3 PLANARITY : 0.006 1137 REMARK 3 DIHEDRAL : 17.235 3809 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 2 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.7027 71.8644 8.5031 REMARK 3 T TENSOR REMARK 3 T11: 0.1258 T22: 0.1943 REMARK 3 T33: 0.2614 T12: 0.0233 REMARK 3 T13: -0.0008 T23: 0.0335 REMARK 3 L TENSOR REMARK 3 L11: 0.7732 L22: 1.9197 REMARK 3 L33: 2.7008 L12: 0.2608 REMARK 3 L13: -1.0320 L23: 0.2373 REMARK 3 S TENSOR REMARK 3 S11: 0.0779 S12: 0.0880 S13: 0.1742 REMARK 3 S21: -0.0022 S22: 0.0247 S23: 0.0324 REMARK 3 S31: -0.1112 S32: -0.2260 S33: -0.0796 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 379 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4243 94.1400 19.8759 REMARK 3 T TENSOR REMARK 3 T11: 0.1392 T22: 0.1323 REMARK 3 T33: 0.1670 T12: -0.0010 REMARK 3 T13: 0.0167 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.8203 L22: 2.4273 REMARK 3 L33: 0.7568 L12: -0.3934 REMARK 3 L13: 0.1276 L23: -0.5110 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: -0.0344 S13: 0.0408 REMARK 3 S21: 0.0505 S22: 0.0397 S23: -0.1076 REMARK 3 S31: -0.0102 S32: 0.0106 S33: -0.0349 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.0882 58.2976 6.1565 REMARK 3 T TENSOR REMARK 3 T11: 0.2178 T22: 0.2138 REMARK 3 T33: 0.2628 T12: 0.0519 REMARK 3 T13: -0.0669 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 1.2626 L22: 2.3346 REMARK 3 L33: 2.4251 L12: -0.6019 REMARK 3 L13: 1.0829 L23: -0.5060 REMARK 3 S TENSOR REMARK 3 S11: 0.1647 S12: 0.1546 S13: -0.0387 REMARK 3 S21: -0.3635 S22: -0.1948 S23: 0.2792 REMARK 3 S31: 0.0308 S32: -0.0050 S33: 0.0494 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 141 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.7823 33.4614 5.3275 REMARK 3 T TENSOR REMARK 3 T11: 0.1188 T22: 0.1195 REMARK 3 T33: 0.0803 T12: -0.0178 REMARK 3 T13: -0.0064 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.0465 L22: 1.3176 REMARK 3 L33: 1.0864 L12: -0.1704 REMARK 3 L13: -0.0848 L23: 0.5058 REMARK 3 S TENSOR REMARK 3 S11: 0.0077 S12: -0.0119 S13: -0.0037 REMARK 3 S21: 0.0108 S22: 0.0079 S23: 0.0775 REMARK 3 S31: 0.0048 S32: 0.0359 S33: -0.0164 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 5WXI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300001859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.8-7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61063 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: APO EARP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH BUFFER (PH 6.8-7.5), REMARK 280 20% PEG3350, 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 48.78900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 97.69400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.78900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 97.69400 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: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -132.0 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 MET A 1 REMARK 465 LYS A 380 REMARK 465 ILE A 381 REMARK 465 ARG A 382 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 GLY B 19 REMARK 465 GLN B 379 REMARK 465 LYS B 380 REMARK 465 ILE B 381 REMARK 465 ARG B 382 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 ASN A 17 CG OD1 ND2 REMARK 470 ASN B 17 CG OD1 ND2 REMARK 470 ARG B 155 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 359 CG CD NE CZ NH1 NH2 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 ASP A 16 43.83 74.38 REMARK 500 ASP A 20 -38.37 70.49 REMARK 500 ALA A 75 143.92 -171.30 REMARK 500 ASN A 178 18.67 -143.13 REMARK 500 SER A 189 144.94 -170.72 REMARK 500 ALA A 240 -124.43 43.50 REMARK 500 ASP B 45 95.63 -164.71 REMARK 500 ALA B 240 -132.60 49.71 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 TRH A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRH B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME B 402 and CYS B REMARK 800 53 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME B 403 and CYS B REMARK 800 158 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide BME B 404 and CYS B REMARK 800 339 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WXJ RELATED DB: PDB REMARK 900 RELATED ID: 5WXK RELATED DB: PDB DBREF 5WXI A 1 382 UNP E6MVV9 E6MVV9_NEIMH 1 382 DBREF 5WXI B 1 382 UNP E6MVV9 E6MVV9_NEIMH 1 382 SEQRES 1 A 382 MET ASN THR PRO PRO PHE VAL CYS TRP ILE PHE CYS LYS SEQRES 2 A 382 VAL ILE ASP ASN PHE GLY ASP ILE GLY VAL SER TRP ARG SEQRES 3 A 382 LEU ALA ARG VAL LEU HIS ARG GLU LEU GLY TRP GLN VAL SEQRES 4 A 382 HIS LEU TRP THR ASP ASP VAL SER ALA LEU ARG ALA LEU SEQRES 5 A 382 CYS PRO ASP LEU PRO ASP VAL PRO CYS VAL HIS GLN ASP SEQRES 6 A 382 ILE HIS VAL ARG THR TRP HIS SER ASP ALA ALA ASP ILE SEQRES 7 A 382 ASP THR ALA PRO VAL PRO ASP VAL VAL ILE GLU THR PHE SEQRES 8 A 382 ALA CYS ASP LEU PRO GLU ASN VAL LEU HIS ILE ILE ARG SEQRES 9 A 382 ARG HIS LYS PRO LEU TRP LEU ASN TRP GLU TYR LEU SER SEQRES 10 A 382 ALA GLU GLU SER ASN GLU ARG LEU HIS LEU MET PRO SER SEQRES 11 A 382 PRO GLN GLU GLY VAL GLN LYS TYR PHE TRP PHE MET GLY SEQRES 12 A 382 PHE SER GLU LYS SER GLY GLY LEU ILE ARG GLU ARG ASP SEQRES 13 A 382 TYR CYS GLU ALA VAL ARG PHE ASP THR GLU ALA LEU ARG SEQRES 14 A 382 GLU ARG LEU MET LEU PRO GLU LYS ASN ALA SER GLU TRP SEQRES 15 A 382 LEU LEU PHE GLY TYR ARG SER ASP VAL TRP ALA LYS TRP SEQRES 16 A 382 LEU GLU MET TRP ARG GLN ALA GLY SER PRO MET THR LEU SEQRES 17 A 382 LEU LEU ALA GLY THR GLN ILE ILE ASP SER LEU LYS GLN SEQRES 18 A 382 SER GLY VAL ILE PRO GLN ASP ALA LEU GLN ASN ASP GLY SEQRES 19 A 382 ASP VAL PHE GLN THR ALA SER VAL ARG LEU VAL LYS ILE SEQRES 20 A 382 PRO PHE VAL PRO GLN GLN ASP PHE ASP GLN LEU LEU HIS SEQRES 21 A 382 LEU ALA ASP CYS ALA VAL ILE ARG GLY GLU ASP SER PHE SEQRES 22 A 382 VAL ARG ALA GLN LEU ALA GLY LYS PRO PHE PHE TRP HIS SEQRES 23 A 382 ILE TYR PRO GLN ASP GLU ASN VAL HIS LEU ASP LYS LEU SEQRES 24 A 382 HIS ALA PHE TRP ASP LYS ALA HIS GLY PHE TYR THR PRO SEQRES 25 A 382 GLU THR VAL SER ALA HIS ARG ARG LEU SER ASP ASP LEU SEQRES 26 A 382 ASN GLY GLY GLU ALA LEU SER ALA THR GLN ARG LEU GLU SEQRES 27 A 382 CYS TRP GLN THR LEU GLN GLN HIS GLN ASN GLY TRP ARG SEQRES 28 A 382 GLN GLY ALA GLU ASP TRP SER ARG TYR LEU PHE GLY GLN SEQRES 29 A 382 PRO SER ALA PRO GLU LYS LEU ALA ALA PHE VAL SER LYS SEQRES 30 A 382 HIS GLN LYS ILE ARG SEQRES 1 B 382 MET ASN THR PRO PRO PHE VAL CYS TRP ILE PHE CYS LYS SEQRES 2 B 382 VAL ILE ASP ASN PHE GLY ASP ILE GLY VAL SER TRP ARG SEQRES 3 B 382 LEU ALA ARG VAL LEU HIS ARG GLU LEU GLY TRP GLN VAL SEQRES 4 B 382 HIS LEU TRP THR ASP ASP VAL SER ALA LEU ARG ALA LEU SEQRES 5 B 382 CYS PRO ASP LEU PRO ASP VAL PRO CYS VAL HIS GLN ASP SEQRES 6 B 382 ILE HIS VAL ARG THR TRP HIS SER ASP ALA ALA ASP ILE SEQRES 7 B 382 ASP THR ALA PRO VAL PRO ASP VAL VAL ILE GLU THR PHE SEQRES 8 B 382 ALA CYS ASP LEU PRO GLU ASN VAL LEU HIS ILE ILE ARG SEQRES 9 B 382 ARG HIS LYS PRO LEU TRP LEU ASN TRP GLU TYR LEU SER SEQRES 10 B 382 ALA GLU GLU SER ASN GLU ARG LEU HIS LEU MET PRO SER SEQRES 11 B 382 PRO GLN GLU GLY VAL GLN LYS TYR PHE TRP PHE MET GLY SEQRES 12 B 382 PHE SER GLU LYS SER GLY GLY LEU ILE ARG GLU ARG ASP SEQRES 13 B 382 TYR CYS GLU ALA VAL ARG PHE ASP THR GLU ALA LEU ARG SEQRES 14 B 382 GLU ARG LEU MET LEU PRO GLU LYS ASN ALA SER GLU TRP SEQRES 15 B 382 LEU LEU PHE GLY TYR ARG SER ASP VAL TRP ALA LYS TRP SEQRES 16 B 382 LEU GLU MET TRP ARG GLN ALA GLY SER PRO MET THR LEU SEQRES 17 B 382 LEU LEU ALA GLY THR GLN ILE ILE ASP SER LEU LYS GLN SEQRES 18 B 382 SER GLY VAL ILE PRO GLN ASP ALA LEU GLN ASN ASP GLY SEQRES 19 B 382 ASP VAL PHE GLN THR ALA SER VAL ARG LEU VAL LYS ILE SEQRES 20 B 382 PRO PHE VAL PRO GLN GLN ASP PHE ASP GLN LEU LEU HIS SEQRES 21 B 382 LEU ALA ASP CYS ALA VAL ILE ARG GLY GLU ASP SER PHE SEQRES 22 B 382 VAL ARG ALA GLN LEU ALA GLY LYS PRO PHE PHE TRP HIS SEQRES 23 B 382 ILE TYR PRO GLN ASP GLU ASN VAL HIS LEU ASP LYS LEU SEQRES 24 B 382 HIS ALA PHE TRP ASP LYS ALA HIS GLY PHE TYR THR PRO SEQRES 25 B 382 GLU THR VAL SER ALA HIS ARG ARG LEU SER ASP ASP LEU SEQRES 26 B 382 ASN GLY GLY GLU ALA LEU SER ALA THR GLN ARG LEU GLU SEQRES 27 B 382 CYS TRP GLN THR LEU GLN GLN HIS GLN ASN GLY TRP ARG SEQRES 28 B 382 GLN GLY ALA GLU ASP TRP SER ARG TYR LEU PHE GLY GLN SEQRES 29 B 382 PRO SER ALA PRO GLU LYS LEU ALA ALA PHE VAL SER LYS SEQRES 30 B 382 HIS GLN LYS ILE ARG HET TRH A 401 35 HET BME A 402 4 HET BME A 403 4 HET BME A 404 4 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET GOL A 409 6 HET TRH B 401 35 HET BME B 402 4 HET BME B 403 4 HET BME B 404 4 HET SO4 B 405 5 HET SO4 B 406 5 HET SO4 B 407 5 HETNAM TRH 2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE HETNAM BME BETA-MERCAPTOETHANOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 TRH 2(C16 H26 N2 O15 P2) FORMUL 4 BME 6(C2 H6 O S) FORMUL 7 SO4 7(O4 S 2-) FORMUL 11 GOL C3 H8 O3 FORMUL 19 HOH *635(H2 O) HELIX 1 AA1 ASP A 20 GLY A 36 1 17 HELIX 2 AA2 ASP A 45 CYS A 53 1 9 HELIX 3 AA3 PRO A 96 LYS A 107 1 12 HELIX 4 AA4 GLU A 119 HIS A 126 1 8 HELIX 5 AA5 ASP A 156 VAL A 161 1 6 HELIX 6 AA6 ASP A 164 LEU A 172 1 9 HELIX 7 AA7 ASP A 190 GLY A 203 1 14 HELIX 8 AA8 THR A 213 SER A 222 1 10 HELIX 9 AA9 PRO A 251 GLN A 253 5 3 HELIX 10 AB1 ASP A 254 ALA A 262 1 9 HELIX 11 AB2 GLU A 270 GLY A 280 1 11 HELIX 12 AB3 GLN A 290 ASN A 293 5 4 HELIX 13 AB4 VAL A 294 HIS A 307 1 14 HELIX 14 AB5 GLY A 308 TYR A 310 5 3 HELIX 15 AB6 THR A 311 ASN A 326 1 16 HELIX 16 AB7 SER A 332 HIS A 346 1 15 HELIX 17 AB8 HIS A 346 GLY A 363 1 18 HELIX 18 AB9 SER A 366 HIS A 378 1 13 HELIX 19 AC1 ILE B 21 GLY B 36 1 16 HELIX 20 AC2 ASP B 45 CYS B 53 1 9 HELIX 21 AC3 PRO B 96 LYS B 107 1 12 HELIX 22 AC4 GLU B 119 HIS B 126 1 8 HELIX 23 AC5 ASP B 156 VAL B 161 1 6 HELIX 24 AC6 ASP B 164 LEU B 172 1 9 HELIX 25 AC7 ASP B 190 GLY B 203 1 14 HELIX 26 AC8 THR B 213 SER B 222 1 10 HELIX 27 AC9 PRO B 251 GLN B 253 5 3 HELIX 28 AD1 ASP B 254 ALA B 262 1 9 HELIX 29 AD2 GLU B 270 GLY B 280 1 11 HELIX 30 AD3 GLN B 290 VAL B 294 5 5 HELIX 31 AD4 HIS B 295 HIS B 307 1 13 HELIX 32 AD5 GLY B 308 TYR B 310 5 3 HELIX 33 AD6 THR B 314 ASN B 326 1 13 HELIX 34 AD7 SER B 332 HIS B 346 1 15 HELIX 35 AD8 HIS B 346 GLY B 363 1 18 HELIX 36 AD9 SER B 366 LYS B 377 1 12 SHEET 1 AA1 8 CYS A 61 HIS A 63 0 SHEET 2 AA1 8 ILE A 66 THR A 70 -1 O VAL A 68 N CYS A 61 SHEET 3 AA1 8 GLN A 38 THR A 43 1 N VAL A 39 O HIS A 67 SHEET 4 AA1 8 VAL A 7 CYS A 12 1 N ILE A 10 O TRP A 42 SHEET 5 AA1 8 VAL A 86 GLU A 89 1 O ILE A 88 N TRP A 9 SHEET 6 AA1 8 LEU A 109 TRP A 113 1 O TRP A 113 N GLU A 89 SHEET 7 AA1 8 VAL A 135 TRP A 140 1 O TYR A 138 N ASN A 112 SHEET 8 AA1 8 PRO A 129 GLN A 132 -1 N GLN A 132 O VAL A 135 SHEET 1 AA2 6 VAL A 236 THR A 239 0 SHEET 2 AA2 6 VAL A 242 LYS A 246 -1 O LEU A 244 N PHE A 237 SHEET 3 AA2 6 MET A 206 LEU A 210 1 N LEU A 210 O VAL A 245 SHEET 4 AA2 6 SER A 180 LEU A 184 1 N TRP A 182 O LEU A 209 SHEET 5 AA2 6 CYS A 264 ARG A 268 1 O VAL A 266 N LEU A 183 SHEET 6 AA2 6 PHE A 283 HIS A 286 1 O HIS A 286 N ILE A 267 SHEET 1 AA3 8 CYS B 61 HIS B 63 0 SHEET 2 AA3 8 ILE B 66 THR B 70 -1 O VAL B 68 N CYS B 61 SHEET 3 AA3 8 GLN B 38 THR B 43 1 N LEU B 41 O HIS B 67 SHEET 4 AA3 8 VAL B 7 CYS B 12 1 N CYS B 8 O HIS B 40 SHEET 5 AA3 8 VAL B 86 GLU B 89 1 O ILE B 88 N TRP B 9 SHEET 6 AA3 8 LEU B 109 TRP B 113 1 O TRP B 113 N GLU B 89 SHEET 7 AA3 8 VAL B 135 TRP B 140 1 O TYR B 138 N ASN B 112 SHEET 8 AA3 8 PRO B 129 GLN B 132 -1 N GLN B 132 O VAL B 135 SHEET 1 AA4 6 VAL B 236 THR B 239 0 SHEET 2 AA4 6 VAL B 242 LYS B 246 -1 O LEU B 244 N PHE B 237 SHEET 3 AA4 6 MET B 206 LEU B 210 1 N LEU B 208 O ARG B 243 SHEET 4 AA4 6 SER B 180 LEU B 184 1 N TRP B 182 O LEU B 209 SHEET 5 AA4 6 CYS B 264 ARG B 268 1 O VAL B 266 N LEU B 183 SHEET 6 AA4 6 PHE B 283 HIS B 286 1 O HIS B 286 N ILE B 267 LINK SG CYS A 53 S2 BME A 402 1555 1555 1.98 LINK SG CYS A 158 S2 BME A 403 1555 1555 1.97 LINK SG CYS A 339 S2 BME A 404 1555 1555 1.95 LINK SG CYS B 53 S2 BME B 402 1555 1555 1.98 LINK SG CYS B 158 S2 BME B 403 1555 1555 1.97 LINK SG CYS B 339 S2 BME B 404 1555 1555 1.94 CISPEP 1 VAL A 59 PRO A 60 0 5.70 CISPEP 2 VAL B 59 PRO B 60 0 5.77 SITE 1 AC1 21 PHE A 18 GLY A 19 ASP A 20 LEU A 52 SITE 2 AC1 21 TYR A 115 TYR A 187 ALA A 211 PHE A 249 SITE 3 AC1 21 VAL A 250 GLN A 252 PHE A 255 ARG A 268 SITE 4 AC1 21 GLY A 269 GLU A 270 ASP A 271 SER A 272 SITE 5 AC1 21 TYR A 288 HOH A 551 HOH A 606 HOH A 715 SITE 6 AC1 21 HOH A 738 SITE 1 AC2 6 TRP A 25 LEU A 52 CYS A 53 GLN A 64 SITE 2 AC2 6 GLN A 252 GLN A 253 SITE 1 AC3 2 TYR A 157 CYS A 158 SITE 1 AC4 4 ARG A 320 GLU A 338 CYS A 339 HOH A 508 SITE 1 AC5 3 HIS A 346 ASN A 348 GLY A 349 SITE 1 AC6 4 VAL A 46 ARG A 50 ASP A 58 VAL A 59 SITE 1 AC7 6 ARG A 200 THR A 239 ALA A 240 HOH A 506 SITE 2 AC7 6 HOH A 707 ARG B 200 SITE 1 AC8 5 PHE A 185 GLY A 212 THR A 213 GLN A 214 SITE 2 AC8 5 ARG A 268 SITE 1 AC9 7 PRO A 60 CYS A 61 VAL A 68 ARG A 69 SITE 2 AC9 7 THR A 80 HOH A 616 ASP B 164 SITE 1 AD1 19 ASP B 16 PHE B 18 ASP B 20 TYR B 115 SITE 2 AD1 19 PHE B 185 TYR B 187 ALA B 211 PHE B 249 SITE 3 AD1 19 VAL B 250 GLN B 252 PHE B 255 ARG B 268 SITE 4 AD1 19 GLY B 269 GLU B 270 ASP B 271 SER B 272 SITE 5 AD1 19 TYR B 288 HOH B 634 HOH B 673 SITE 1 AD2 4 GLY B 212 THR B 213 GLN B 214 ARG B 268 SITE 1 AD3 6 HIS B 346 ASN B 348 GLY B 349 HOH B 602 SITE 2 AD3 6 HOH B 649 HOH B 684 SITE 1 AD4 4 VAL B 46 ARG B 50 ASP B 58 VAL B 59 SITE 1 AD5 9 LEU B 49 ARG B 50 ALA B 51 LEU B 52 SITE 2 AD5 9 PRO B 54 ASP B 55 LEU B 56 GLN B 64 SITE 3 AD5 9 GLN B 252 SITE 1 AD6 6 ASP B 156 TYR B 157 GLU B 159 ALA B 160 SITE 2 AD6 6 VAL B 161 HOH B 637 SITE 1 AD7 12 ALA B 317 ARG B 320 LEU B 321 GLN B 335 SITE 2 AD7 12 ARG B 336 LEU B 337 GLU B 338 TRP B 340 SITE 3 AD7 12 GLN B 341 THR B 342 LEU B 343 HOH B 656 CRYST1 97.578 195.388 46.366 90.00 90.00 90.00 P 21 21 2 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 0.010248 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005118 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021568 0.00000