HEADER HYDROLASE 03-APR-08 3CQM OBSLTE 04-AUG-10 3CQM 3NVD TITLE STRUCTURE OF YBBD IN COMPLEX WITH PUGNAC COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED LIPOPROTEIN YBBD; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ORF1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 STRAIN: WT168; SOURCE 5 GENE: YBBD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B KEYWDS BETA-N-HEXOSAMINIDASE, BACILLUS SUBTILIS, TIM BARREL, GLYCOSIDASE, KEYWDS 2 HYDROLASE, LIPOPROTEIN, MEMBRANE, PALMITATE EXPDTA X-RAY DIFFRACTION AUTHOR S.FISCHER REVDAT 3 04-AUG-10 3CQM 1 OBSLTE REVDAT 2 19-JAN-10 3CQM 1 REMARK REVDAT 1 07-APR-09 3CQM 0 JRNL AUTH S.LITZINGER,S.FISCHER,W.WELTE,K.DIEDERICHS,C.MAYER JRNL TITL BETA-N-HEXOSAMINIDASE (YBBD) FROM BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 127623 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.520 REMARK 3 FREE R VALUE TEST SET COUNT : 7045 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 48.5660 - 4.6030 0.98 5847 328 0.1850 0.2090 REMARK 3 2 4.6030 - 3.6540 0.98 5737 311 0.1720 0.2100 REMARK 3 3 3.6540 - 3.1920 0.98 5897 280 0.1910 0.2350 REMARK 3 4 3.1920 - 2.9000 0.98 6025 307 0.2050 0.2530 REMARK 3 5 2.9000 - 2.6930 0.98 6140 344 0.2090 0.2590 REMARK 3 6 2.6930 - 2.5340 0.98 6237 322 0.2130 0.2590 REMARK 3 7 2.5340 - 2.4070 0.98 6341 372 0.2150 0.2380 REMARK 3 8 2.4070 - 2.3020 0.98 6293 359 0.2150 0.2760 REMARK 3 9 2.3020 - 2.2140 0.98 6351 307 0.2200 0.2730 REMARK 3 10 2.2140 - 2.1370 0.98 6367 343 0.2240 0.2830 REMARK 3 11 2.1370 - 2.0700 0.98 6394 347 0.2230 0.2920 REMARK 3 12 2.0700 - 2.0110 0.98 6358 328 0.2280 0.2910 REMARK 3 13 2.0110 - 1.9580 0.98 6352 352 0.2360 0.2690 REMARK 3 14 1.9580 - 1.9100 0.98 6197 315 0.2510 0.3170 REMARK 3 15 1.9100 - 1.8670 0.98 6254 305 0.2550 0.2790 REMARK 3 16 1.8670 - 1.8270 0.98 6252 318 0.2660 0.3420 REMARK 3 17 1.8270 - 1.7910 0.98 6181 318 0.2730 0.2980 REMARK 3 18 1.7910 - 1.7570 0.98 6093 318 0.2800 0.3270 REMARK 3 19 1.7570 - 1.7250 0.98 5627 304 0.2900 0.3180 REMARK 3 20 1.7255 - 1.6963 0.98 4281 221 0.3030 0.3629 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60200 REMARK 3 B22 (A**2) : 1.07170 REMARK 3 B33 (A**2) : -2.63640 REMARK 3 B12 (A**2) : 0.42590 REMARK 3 B13 (A**2) : 3.00230 REMARK 3 B23 (A**2) : -4.32330 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: 0.1770 REMARK 3 OPERATOR: H,-K,H-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.003 9776 REMARK 3 ANGLE : 0.757 13193 REMARK 3 CHIRALITY : 0.048 1488 REMARK 3 PLANARITY : 0.003 1710 REMARK 3 DIHEDRAL : 17.350 3736 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 67.7966 57.7669 85.5826 REMARK 3 T TENSOR REMARK 3 T11: 0.0225 T22: -0.0072 REMARK 3 T33: 0.0179 T12: -0.0050 REMARK 3 T13: -0.0152 T23: 0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.0159 L22: 0.0032 REMARK 3 L33: 0.0333 L12: 0.0099 REMARK 3 L13: -0.0100 L23: -0.0053 REMARK 3 S TENSOR REMARK 3 S11: 0.0104 S12: -0.0069 S13: -0.0133 REMARK 3 S21: 0.0068 S22: -0.0024 S23: -0.0095 REMARK 3 S31: -0.0134 S32: -0.0003 S33: 0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 37.4661 43.6012 49.0593 REMARK 3 T TENSOR REMARK 3 T11: 0.0276 T22: 0.0525 REMARK 3 T33: 0.0400 T12: -0.0091 REMARK 3 T13: -0.0060 T23: -0.0094 REMARK 3 L TENSOR REMARK 3 L11: 0.0094 L22: 0.1442 REMARK 3 L33: 0.1919 L12: -0.0706 REMARK 3 L13: -0.0801 L23: 0.1288 REMARK 3 S TENSOR REMARK 3 S11: 0.0065 S12: 0.0278 S13: -0.0057 REMARK 3 S21: 0.0092 S22: -0.0150 S23: -0.0135 REMARK 3 S31: 0.0027 S32: 0.0264 S33: 0.0047 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 3CQM COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-08. REMARK 100 THE RCSB ID CODE IS RCSB047094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127623 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.696 REMARK 200 RESOLUTION RANGE LOW (A) : 48.549 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 1.930 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3BMX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 27% PEG 1000, PH REMARK 280 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K 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, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 PRO A 3 REMARK 465 VAL A 4 REMARK 465 PHE A 5 REMARK 465 PRO A 6 REMARK 465 LEU A 7 REMARK 465 ILE A 8 REMARK 465 LEU A 9 REMARK 465 SER A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 LEU A 13 REMARK 465 PHE A 14 REMARK 465 LEU A 15 REMARK 465 SER A 16 REMARK 465 CYS A 17 REMARK 465 PHE A 18 REMARK 465 PHE A 19 REMARK 465 GLY A 20 REMARK 465 ALA A 21 REMARK 465 ARG A 22 REMARK 465 GLN A 23 REMARK 465 THR A 24 REMARK 465 GLU A 25 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 PRO B 3 REMARK 465 VAL B 4 REMARK 465 PHE B 5 REMARK 465 PRO B 6 REMARK 465 LEU B 7 REMARK 465 ILE B 8 REMARK 465 LEU B 9 REMARK 465 SER B 10 REMARK 465 ALA B 11 REMARK 465 VAL B 12 REMARK 465 LEU B 13 REMARK 465 PHE B 14 REMARK 465 LEU B 15 REMARK 465 SER B 16 REMARK 465 CYS B 17 REMARK 465 PHE B 18 REMARK 465 PHE B 19 REMARK 465 GLY B 20 REMARK 465 ALA B 21 REMARK 465 ARG B 22 REMARK 465 GLN B 23 REMARK 465 THR B 24 REMARK 465 GLU B 25 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 477 CE NZ REMARK 480 ARG B 478 CD NE 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 PHE A 138 160.20 65.45 REMARK 500 ARG A 148 -52.53 74.02 REMARK 500 ILE A 188 -78.36 -90.79 REMARK 500 VAL A 250 -78.83 -122.44 REMARK 500 GLN A 307 -63.38 -95.48 REMARK 500 TYR A 399 108.93 -161.80 REMARK 500 ASN A 440 70.22 -159.49 REMARK 500 LYS A 448 78.85 -115.89 REMARK 500 VAL A 517 -84.90 -92.39 REMARK 500 ASP A 534 -151.53 -104.40 REMARK 500 ARG A 563 -108.98 -121.53 REMARK 500 PHE A 571 54.07 -143.07 REMARK 500 ASP B 123 58.58 -102.02 REMARK 500 PHE B 138 163.31 64.64 REMARK 500 ILE B 188 -74.85 -91.36 REMARK 500 PRO B 224 34.63 -95.74 REMARK 500 VAL B 250 -79.31 -107.97 REMARK 500 LEU B 304 -69.43 -91.61 REMARK 500 ASN B 440 79.16 -159.48 REMARK 500 VAL B 517 -79.34 -91.26 REMARK 500 ASP B 534 -161.04 -116.26 REMARK 500 ARG B 563 -112.64 -116.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 647 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 NA A 643 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 318 OD2 REMARK 620 2 SER A 233 OG 107.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 643 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 318 OD2 REMARK 620 2 SER B 233 OG 102.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 643 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 644 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 645 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 643 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 644 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 645 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAN A 646 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 647 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAN B 646 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BMX RELATED DB: PDB REMARK 900 BETA-N-HEXOSAMINIDASE (YBBD) FROM BACILLUS SUBTILIS DBREF 3CQM A 1 642 UNP P40406 YBBD_BACSU 1 642 DBREF 3CQM B 1 642 UNP P40406 YBBD_BACSU 1 642 SEQRES 1 A 642 MET ARG PRO VAL PHE PRO LEU ILE LEU SER ALA VAL LEU SEQRES 2 A 642 PHE LEU SER CYS PHE PHE GLY ALA ARG GLN THR GLU ALA SEQRES 3 A 642 SER ALA SER LYS ARG ALA ILE ASP ALA ASN GLN ILE VAL SEQRES 4 A 642 ASN ARG MET SER LEU ASP GLU LYS LEU GLY GLN MET LEU SEQRES 5 A 642 MET PRO ASP PHE ARG ASN TRP GLN LYS GLU GLY GLU SER SEQRES 6 A 642 SER PRO GLN ALA LEU THR LYS MET ASN ASP GLU VAL ALA SEQRES 7 A 642 SER LEU VAL LYS LYS TYR GLN PHE GLY GLY ILE ILE LEU SEQRES 8 A 642 PHE ALA GLU ASN VAL LYS THR THR LYS GLN THR VAL GLN SEQRES 9 A 642 LEU THR ASP ASP TYR GLN LYS ALA SER PRO LYS ILE PRO SEQRES 10 A 642 LEU MET LEU SER ILE ASP GLN GLU GLY GLY ILE VAL THR SEQRES 11 A 642 ARG LEU GLY GLU GLY THR ASN PHE PRO GLY ASN MET ALA SEQRES 12 A 642 LEU GLY ALA ALA ARG SER ARG ILE ASN ALA TYR GLN THR SEQRES 13 A 642 GLY SER ILE ILE GLY LYS GLU LEU SER ALA LEU GLY ILE SEQRES 14 A 642 ASN THR ASP PHE SER PRO VAL VAL ASP ILE ASN ASN ASN SEQRES 15 A 642 PRO ASP ASN PRO VAL ILE GLY VAL ARG SER PHE SER SER SEQRES 16 A 642 ASN ARG GLU LEU THR SER ARG LEU GLY LEU TYR THR MET SEQRES 17 A 642 LYS GLY LEU GLN ARG GLN ASP ILE ALA SER ALA LEU LYS SEQRES 18 A 642 HIS PHE PRO GLY HIS GLY ASP THR ASP VAL ASP SER HIS SEQRES 19 A 642 TYR GLY LEU PRO LEU VAL SER HIS GLY GLN GLU ARG LEU SEQRES 20 A 642 ARG GLU VAL GLU LEU TYR PRO PHE GLN LYS ALA ILE ASP SEQRES 21 A 642 ALA GLY ALA ASP MET VAL MET THR ALA HIS VAL GLN PHE SEQRES 22 A 642 PRO ALA PHE ASP ASP THR THR TYR LYS SER LYS LEU ASP SEQRES 23 A 642 GLY SER ASP ILE LEU VAL PRO ALA THR LEU SER LYS LYS SEQRES 24 A 642 VAL MET THR GLY LEU LEU ARG GLN GLU MET GLY PHE ASN SEQRES 25 A 642 GLY VAL ILE VAL THR ASP ALA LEU ASN MET LYS ALA ILE SEQRES 26 A 642 ALA ASP HIS PHE GLY GLN GLU GLU ALA VAL VAL MET ALA SEQRES 27 A 642 VAL LYS ALA GLY VAL ASP ILE ALA LEU MET PRO ALA SER SEQRES 28 A 642 VAL THR SER LEU LYS GLU GLU GLN LYS PHE ALA ARG VAL SEQRES 29 A 642 ILE GLN ALA LEU LYS GLU ALA VAL LYS ASN GLY ASP ILE SEQRES 30 A 642 PRO GLU GLN GLN ILE ASN ASN SER VAL GLU ARG ILE ILE SEQRES 31 A 642 SER LEU LYS ILE LYS ARG GLY MET TYR PRO ALA ARG ASN SEQRES 32 A 642 SER ASP SER THR LYS GLU LYS ILE ALA LYS ALA LYS LYS SEQRES 33 A 642 ILE VAL GLY SER LYS GLN HIS LEU LYS ALA GLU LYS LYS SEQRES 34 A 642 LEU ALA GLU LYS ALA VAL THR VAL LEU LYS ASN GLU GLN SEQRES 35 A 642 HIS THR LEU PRO PHE LYS PRO LYS LYS GLY SER ARG ILE SEQRES 36 A 642 LEU ILE VAL ALA PRO TYR GLU GLU GLN THR ALA SER ILE SEQRES 37 A 642 GLU GLN THR ILE HIS ASP LEU ILE LYS ARG LYS LYS ILE SEQRES 38 A 642 LYS PRO VAL SER LEU SER LYS MET ASN PHE ALA SER GLN SEQRES 39 A 642 VAL PHE LYS THR GLU HIS GLU LYS GLN VAL LYS GLU ALA SEQRES 40 A 642 ASP TYR ILE ILE THR GLY SER TYR VAL VAL LYS ASN ASP SEQRES 41 A 642 PRO VAL VAL ASN ASP GLY VAL ILE ASP ASP THR ILE SER SEQRES 42 A 642 ASP SER SER LYS TRP ALA THR VAL PHE PRO ARG ALA VAL SEQRES 43 A 642 MET LYS ALA ALA LEU GLN HIS ASN LYS PRO PHE VAL LEU SEQRES 44 A 642 MET SER LEU ARG ASN PRO TYR ASP ALA ALA ASN PHE GLU SEQRES 45 A 642 GLU ALA LYS ALA LEU ILE ALA VAL TYR GLY PHE LYS GLY SEQRES 46 A 642 TYR ALA ASN GLY ARG TYR LEU GLN PRO ASN ILE PRO ALA SEQRES 47 A 642 GLY VAL MET ALA ILE PHE GLY GLN ALA LYS PRO LYS GLY SEQRES 48 A 642 THR LEU PRO VAL ASP ILE PRO SER VAL THR LYS PRO GLY SEQRES 49 A 642 ASN THR LEU TYR PRO LEU GLY TYR GLY LEU ASN ILE LYS SEQRES 50 A 642 THR GLY ARG PRO LEU SEQRES 1 B 642 MET ARG PRO VAL PHE PRO LEU ILE LEU SER ALA VAL LEU SEQRES 2 B 642 PHE LEU SER CYS PHE PHE GLY ALA ARG GLN THR GLU ALA SEQRES 3 B 642 SER ALA SER LYS ARG ALA ILE ASP ALA ASN GLN ILE VAL SEQRES 4 B 642 ASN ARG MET SER LEU ASP GLU LYS LEU GLY GLN MET LEU SEQRES 5 B 642 MET PRO ASP PHE ARG ASN TRP GLN LYS GLU GLY GLU SER SEQRES 6 B 642 SER PRO GLN ALA LEU THR LYS MET ASN ASP GLU VAL ALA SEQRES 7 B 642 SER LEU VAL LYS LYS TYR GLN PHE GLY GLY ILE ILE LEU SEQRES 8 B 642 PHE ALA GLU ASN VAL LYS THR THR LYS GLN THR VAL GLN SEQRES 9 B 642 LEU THR ASP ASP TYR GLN LYS ALA SER PRO LYS ILE PRO SEQRES 10 B 642 LEU MET LEU SER ILE ASP GLN GLU GLY GLY ILE VAL THR SEQRES 11 B 642 ARG LEU GLY GLU GLY THR ASN PHE PRO GLY ASN MET ALA SEQRES 12 B 642 LEU GLY ALA ALA ARG SER ARG ILE ASN ALA TYR GLN THR SEQRES 13 B 642 GLY SER ILE ILE GLY LYS GLU LEU SER ALA LEU GLY ILE SEQRES 14 B 642 ASN THR ASP PHE SER PRO VAL VAL ASP ILE ASN ASN ASN SEQRES 15 B 642 PRO ASP ASN PRO VAL ILE GLY VAL ARG SER PHE SER SER SEQRES 16 B 642 ASN ARG GLU LEU THR SER ARG LEU GLY LEU TYR THR MET SEQRES 17 B 642 LYS GLY LEU GLN ARG GLN ASP ILE ALA SER ALA LEU LYS SEQRES 18 B 642 HIS PHE PRO GLY HIS GLY ASP THR ASP VAL ASP SER HIS SEQRES 19 B 642 TYR GLY LEU PRO LEU VAL SER HIS GLY GLN GLU ARG LEU SEQRES 20 B 642 ARG GLU VAL GLU LEU TYR PRO PHE GLN LYS ALA ILE ASP SEQRES 21 B 642 ALA GLY ALA ASP MET VAL MET THR ALA HIS VAL GLN PHE SEQRES 22 B 642 PRO ALA PHE ASP ASP THR THR TYR LYS SER LYS LEU ASP SEQRES 23 B 642 GLY SER ASP ILE LEU VAL PRO ALA THR LEU SER LYS LYS SEQRES 24 B 642 VAL MET THR GLY LEU LEU ARG GLN GLU MET GLY PHE ASN SEQRES 25 B 642 GLY VAL ILE VAL THR ASP ALA LEU ASN MET LYS ALA ILE SEQRES 26 B 642 ALA ASP HIS PHE GLY GLN GLU GLU ALA VAL VAL MET ALA SEQRES 27 B 642 VAL LYS ALA GLY VAL ASP ILE ALA LEU MET PRO ALA SER SEQRES 28 B 642 VAL THR SER LEU LYS GLU GLU GLN LYS PHE ALA ARG VAL SEQRES 29 B 642 ILE GLN ALA LEU LYS GLU ALA VAL LYS ASN GLY ASP ILE SEQRES 30 B 642 PRO GLU GLN GLN ILE ASN ASN SER VAL GLU ARG ILE ILE SEQRES 31 B 642 SER LEU LYS ILE LYS ARG GLY MET TYR PRO ALA ARG ASN SEQRES 32 B 642 SER ASP SER THR LYS GLU LYS ILE ALA LYS ALA LYS LYS SEQRES 33 B 642 ILE VAL GLY SER LYS GLN HIS LEU LYS ALA GLU LYS LYS SEQRES 34 B 642 LEU ALA GLU LYS ALA VAL THR VAL LEU LYS ASN GLU GLN SEQRES 35 B 642 HIS THR LEU PRO PHE LYS PRO LYS LYS GLY SER ARG ILE SEQRES 36 B 642 LEU ILE VAL ALA PRO TYR GLU GLU GLN THR ALA SER ILE SEQRES 37 B 642 GLU GLN THR ILE HIS ASP LEU ILE LYS ARG LYS LYS ILE SEQRES 38 B 642 LYS PRO VAL SER LEU SER LYS MET ASN PHE ALA SER GLN SEQRES 39 B 642 VAL PHE LYS THR GLU HIS GLU LYS GLN VAL LYS GLU ALA SEQRES 40 B 642 ASP TYR ILE ILE THR GLY SER TYR VAL VAL LYS ASN ASP SEQRES 41 B 642 PRO VAL VAL ASN ASP GLY VAL ILE ASP ASP THR ILE SER SEQRES 42 B 642 ASP SER SER LYS TRP ALA THR VAL PHE PRO ARG ALA VAL SEQRES 43 B 642 MET LYS ALA ALA LEU GLN HIS ASN LYS PRO PHE VAL LEU SEQRES 44 B 642 MET SER LEU ARG ASN PRO TYR ASP ALA ALA ASN PHE GLU SEQRES 45 B 642 GLU ALA LYS ALA LEU ILE ALA VAL TYR GLY PHE LYS GLY SEQRES 46 B 642 TYR ALA ASN GLY ARG TYR LEU GLN PRO ASN ILE PRO ALA SEQRES 47 B 642 GLY VAL MET ALA ILE PHE GLY GLN ALA LYS PRO LYS GLY SEQRES 48 B 642 THR LEU PRO VAL ASP ILE PRO SER VAL THR LYS PRO GLY SEQRES 49 B 642 ASN THR LEU TYR PRO LEU GLY TYR GLY LEU ASN ILE LYS SEQRES 50 B 642 THR GLY ARG PRO LEU HET OAN A 646 25 HET PG4 A 647 11 HET NA A 643 1 HET ACT A 644 4 HET ACT A 645 4 HET OAN B 646 25 HET NA B 643 1 HET ACT B 644 4 HET ACT B 645 4 HETNAM OAN O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N- HETNAM 2 OAN PHENYLCARBAMATE HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM NA SODIUM ION HETNAM ACT ACETATE ION FORMUL 3 OAN 2(C15 H19 N3 O7) FORMUL 4 PG4 C8 H18 O5 FORMUL 5 NA 2(NA 1+) FORMUL 6 ACT 4(C2 H3 O2 1-) FORMUL 12 HOH *1254(H2 O) HELIX 1 1 ALA A 26 ARG A 41 1 16 HELIX 2 2 SER A 43 MET A 51 1 9 HELIX 3 3 ASN A 74 GLN A 85 1 12 HELIX 4 4 PHE A 92 VAL A 96 5 5 HELIX 5 5 THR A 98 SER A 113 1 16 HELIX 6 6 GLY A 140 ARG A 148 1 9 HELIX 7 7 SER A 149 GLY A 168 1 20 HELIX 8 8 ILE A 188 SER A 192 5 5 HELIX 9 9 ASN A 196 GLN A 214 1 19 HELIX 10 10 GLY A 243 VAL A 250 1 8 HELIX 11 11 LEU A 252 ALA A 261 1 10 HELIX 12 12 PRO A 293 LEU A 296 5 4 HELIX 13 13 SER A 297 THR A 302 1 6 HELIX 14 14 MET A 322 ASP A 327 1 6 HELIX 15 15 GLY A 330 GLY A 342 1 13 HELIX 16 16 SER A 354 GLU A 357 5 4 HELIX 17 17 GLU A 358 GLY A 375 1 18 HELIX 18 18 PRO A 378 ARG A 396 1 19 HELIX 19 19 SER A 406 VAL A 418 1 13 HELIX 20 20 SER A 420 VAL A 435 1 16 HELIX 21 21 GLN A 442 THR A 444 5 3 HELIX 22 22 TYR A 461 ARG A 478 1 18 HELIX 23 23 LYS A 497 ALA A 507 1 11 HELIX 24 24 LYS A 537 HIS A 553 1 17 HELIX 25 25 ASN A 564 PHE A 571 5 8 HELIX 26 26 PRO A 594 PHE A 604 1 11 HELIX 27 27 ALA B 26 ARG B 41 1 16 HELIX 28 28 SER B 43 MET B 51 1 9 HELIX 29 29 ASN B 74 GLN B 85 1 12 HELIX 30 30 PHE B 92 VAL B 96 5 5 HELIX 31 31 THR B 98 SER B 113 1 16 HELIX 32 32 GLY B 140 ARG B 148 1 9 HELIX 33 33 SER B 149 LEU B 167 1 19 HELIX 34 34 ILE B 188 SER B 192 5 5 HELIX 35 35 ASN B 196 GLN B 214 1 19 HELIX 36 36 GLY B 243 VAL B 250 1 8 HELIX 37 37 LEU B 252 ALA B 261 1 10 HELIX 38 38 PRO B 293 LEU B 296 5 4 HELIX 39 39 SER B 297 THR B 302 1 6 HELIX 40 40 MET B 322 ASP B 327 1 6 HELIX 41 41 GLY B 330 GLY B 342 1 13 HELIX 42 42 SER B 354 GLU B 357 5 4 HELIX 43 43 GLU B 358 GLY B 375 1 18 HELIX 44 44 PRO B 378 ARG B 396 1 19 HELIX 45 45 SER B 406 VAL B 418 1 13 HELIX 46 46 SER B 420 VAL B 435 1 16 HELIX 47 47 GLN B 442 THR B 444 5 3 HELIX 48 48 TYR B 461 ARG B 478 1 18 HELIX 49 49 LYS B 497 ALA B 507 1 11 HELIX 50 50 LYS B 537 HIS B 553 1 17 HELIX 51 51 ASN B 564 PHE B 571 5 8 HELIX 52 52 PRO B 594 PHE B 604 1 11 SHEET 1 A 2 LEU A 52 MET A 53 0 SHEET 2 A 2 ALA A 346 LEU A 347 1 O ALA A 346 N MET A 53 SHEET 1 B 2 ASN A 58 TRP A 59 0 SHEET 2 B 2 GLN A 68 ALA A 69 -1 O GLN A 68 N TRP A 59 SHEET 1 C 6 GLY A 88 LEU A 91 0 SHEET 2 C 6 MET A 119 ILE A 122 1 O SER A 121 N LEU A 91 SHEET 3 C 6 THR A 171 ASP A 172 1 O THR A 171 N LEU A 120 SHEET 4 C 6 ALA A 217 PHE A 223 1 O ALA A 217 N ASP A 172 SHEET 5 C 6 MET A 265 THR A 268 1 O MET A 267 N LEU A 220 SHEET 6 C 6 VAL A 314 VAL A 316 1 O VAL A 316 N VAL A 266 SHEET 1 D 2 THR A 280 LYS A 282 0 SHEET 2 D 2 ASP A 289 LEU A 291 -1 O ILE A 290 N TYR A 281 SHEET 1 E 6 THR A 436 ASN A 440 0 SHEET 2 E 6 ALA A 576 ALA A 579 -1 O LEU A 577 N LEU A 438 SHEET 3 E 6 PHE A 557 SER A 561 1 N SER A 561 O ILE A 578 SHEET 4 E 6 TYR A 509 SER A 514 1 N THR A 512 O MET A 560 SHEET 5 E 6 ARG A 454 ALA A 459 1 N VAL A 458 O ILE A 511 SHEET 6 E 6 SER A 485 ASN A 490 1 O SER A 487 N ILE A 457 SHEET 1 F 2 VAL A 523 ASN A 524 0 SHEET 2 F 2 VAL A 527 ILE A 528 -1 O VAL A 527 N ASN A 524 SHEET 1 G 2 TYR A 586 ALA A 587 0 SHEET 2 G 2 ARG A 590 TYR A 591 -1 O ARG A 590 N ALA A 587 SHEET 1 H 2 ILE A 617 PRO A 618 0 SHEET 2 H 2 THR A 626 TYR A 628 -1 O LEU A 627 N ILE A 617 SHEET 1 I 2 LEU B 52 MET B 53 0 SHEET 2 I 2 ALA B 346 LEU B 347 1 O ALA B 346 N MET B 53 SHEET 1 J 2 ASN B 58 TRP B 59 0 SHEET 2 J 2 GLN B 68 ALA B 69 -1 O GLN B 68 N TRP B 59 SHEET 1 K 6 GLY B 88 LEU B 91 0 SHEET 2 K 6 MET B 119 ILE B 122 1 O SER B 121 N LEU B 91 SHEET 3 K 6 THR B 171 ASP B 172 1 O THR B 171 N LEU B 120 SHEET 4 K 6 ALA B 217 PHE B 223 1 O ALA B 217 N ASP B 172 SHEET 5 K 6 MET B 265 THR B 268 1 O MET B 267 N LEU B 220 SHEET 6 K 6 VAL B 314 VAL B 316 1 O VAL B 316 N VAL B 266 SHEET 1 L 2 THR B 280 LYS B 282 0 SHEET 2 L 2 ASP B 289 LEU B 291 -1 O ILE B 290 N TYR B 281 SHEET 1 M 6 THR B 436 ASN B 440 0 SHEET 2 M 6 ALA B 576 ALA B 579 -1 O ALA B 579 N THR B 436 SHEET 3 M 6 PHE B 557 SER B 561 1 N SER B 561 O ILE B 578 SHEET 4 M 6 TYR B 509 SER B 514 1 N THR B 512 O MET B 560 SHEET 5 M 6 SER B 453 ALA B 459 1 N VAL B 458 O ILE B 511 SHEET 6 M 6 VAL B 484 ASN B 490 1 O SER B 487 N ILE B 457 SHEET 1 N 2 VAL B 523 ASN B 524 0 SHEET 2 N 2 VAL B 527 ILE B 528 -1 O VAL B 527 N ASN B 524 SHEET 1 O 2 TYR B 586 ALA B 587 0 SHEET 2 O 2 ARG B 590 TYR B 591 -1 O ARG B 590 N ALA B 587 SHEET 1 P 2 ILE B 617 PRO B 618 0 SHEET 2 P 2 THR B 626 TYR B 628 -1 O TYR B 628 N ILE B 617 LINK OD2 ASP A 318 NA NA A 643 1555 1555 2.97 LINK OD2 ASP B 318 NA NA B 643 1555 1555 2.91 LINK OG SER A 233 NA NA A 643 1555 1555 3.03 LINK OG SER B 233 NA NA B 643 1555 1555 3.10 CISPEP 1 SER A 174 PRO A 175 0 8.98 CISPEP 2 LYS A 221 HIS A 222 0 0.25 CISPEP 3 PHE A 223 PRO A 224 0 10.92 CISPEP 4 TYR A 399 PRO A 400 0 2.13 CISPEP 5 LEU A 445 PRO A 446 0 -0.06 CISPEP 6 SER B 174 PRO B 175 0 5.44 CISPEP 7 LYS B 221 HIS B 222 0 -6.54 CISPEP 8 PHE B 223 PRO B 224 0 1.73 CISPEP 9 TYR B 399 PRO B 400 0 2.92 CISPEP 10 LEU B 445 PRO B 446 0 1.14 SITE 1 AC1 5 HIS A 226 SER A 233 ALA A 269 HIS A 270 SITE 2 AC1 5 ASP A 318 SITE 1 AC2 4 PRO A 274 ASP A 277 ASP A 278 LYS A 299 SITE 1 AC3 6 GLN A 272 ASP A 289 ILE A 290 LEU A 291 SITE 2 AC3 6 LYS A 477 ARG A 478 SITE 1 AC4 5 HIS B 226 SER B 233 ALA B 269 HIS B 270 SITE 2 AC4 5 ASP B 318 SITE 1 AC5 5 ASP B 230 VAL B 231 PRO B 238 LEU B 239 SITE 2 AC5 5 HOH B 912 SITE 1 AC6 4 ASN B 181 HIS B 242 ARG B 246 GLU B 251 SITE 1 AC7 15 ILE A 90 PHE A 92 ASP A 123 VAL A 187 SITE 2 AC7 15 ARG A 191 LYS A 221 HIS A 222 SER A 233 SITE 3 AC7 15 HIS A 234 MET A 267 ASP A 318 ALA A 319 SITE 4 AC7 15 ASN A 321 MET A 322 HOH A 819 SITE 1 AC8 9 ASP A 34 ILE A 38 ILE A 394 TYR A 399 SITE 2 AC8 9 ASP A 530 THR A 531 ILE A 532 SER A 533 SITE 3 AC8 9 HOH A1034 SITE 1 AC9 17 ARG B 57 ILE B 90 PHE B 92 ASP B 123 SITE 2 AC9 17 VAL B 187 ARG B 191 LYS B 221 HIS B 222 SITE 3 AC9 17 SER B 233 HIS B 234 MET B 267 ASP B 318 SITE 4 AC9 17 ALA B 319 ASN B 321 MET B 322 MET B 348 SITE 5 AC9 17 HOH B1011 CRYST1 58.480 73.210 83.790 79.82 69.44 88.23 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 0.017100 -0.000528 -0.006422 0.00000 SCALE2 0.000000 0.013666 -0.002461 0.00000 SCALE3 0.000000 0.000000 0.012952 0.00000