PDB Short entry for 1VFU HEADER HYDROLASE 19-APR-04 1VFU TITLE CRYSTAL STRUCTURE OF THERMOACTINOMYCES VULGARIS R-47 AMYLASE 2/GAMMA- TITLE 2 CYCLODEXTRIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEOPULLULANASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALPHA-AMYLASE 2, ALPHA-AMYLASE II; COMPND 5 EC: 3.2.1.135; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOACTINOMYCES VULGARIS; SOURCE 3 ORGANISM_TAXID: 2026; SOURCE 4 STRAIN: R-47; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMYLASE, COMPLEX, CYCLODEXTRIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.OHTAKI,M.MIZUNO,T.TONOZUKA,Y.SAKANO,S.KAMITORI REVDAT 5 27-DEC-23 1VFU 1 REMARK REVDAT 4 10-NOV-21 1VFU 1 SEQADV HETSYN REVDAT 3 29-JUL-20 1VFU 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 24-FEB-09 1VFU 1 VERSN REVDAT 1 08-FEB-05 1VFU 0 JRNL AUTH A.OHTAKI,M.MIZUNO,T.TONOZUKA,Y.SAKANO,S.KAMITORI JRNL TITL COMPLEX STRUCTURES OF THERMOACTINOMYCES VULGARIS R-47 JRNL TITL 2 ALPHA-AMYLASE 2 WITH ACARBOSE AND CYCLODEXTRINS DEMONSTRATE JRNL TITL 3 THE MULTIPLE SUBSTRATE RECOGNITION MECHANISM JRNL REF J.BIOL.CHEM. V. 279 31033 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15138257 JRNL DOI 10.1074/JBC.M404311200 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3989764.150 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 26435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2620 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3848 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 444 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 178 REMARK 3 SOLVENT ATOMS : 133 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 13.66000 REMARK 3 B22 (A**2) : -3.46000 REMARK 3 B33 (A**2) : -10.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.63 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.900 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 51.28 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000006569. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26454 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 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 <I/SIGMA(I)> 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: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG20000, CALCIUM CHLORIDE, MES, PH REMARK 280 6.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 56.72700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.04000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.24800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.04000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 56.72700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.24800 REMARK 290 SMTRY3 4 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 APPLY THE FOLLOWING TO CHAINS: B, D 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 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 ALA A 510 O HOH A 1056 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 PRO A 466 C - N - CA ANGL. DEV. = -17.8 DEGREES REMARK 500 PRO B 138 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 PRO B 138 C - N - CD ANGL. DEV. = -13.6 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 A 2 94.03 -51.19 REMARK 500 HIS A 8 150.72 178.17 REMARK 500 ALA A 10 52.21 -61.48 REMARK 500 LYS A 11 -178.35 -175.20 REMARK 500 ALA A 15 93.31 -162.77 REMARK 500 SER A 19 -176.09 -174.31 REMARK 500 ALA A 42 154.76 177.30 REMARK 500 GLU A 49 49.73 -81.02 REMARK 500 ALA A 55 122.40 178.54 REMARK 500 LYS A 59 99.06 -65.93 REMARK 500 ASP A 63 -152.93 -93.30 REMARK 500 ARG A 65 -18.78 -159.95 REMARK 500 ALA A 93 173.05 -57.40 REMARK 500 GLU A 98 -14.81 -48.67 REMARK 500 ARG A 105 -53.64 -27.68 REMARK 500 TYR A 113 79.07 -114.46 REMARK 500 ALA A 114 -71.73 -19.54 REMARK 500 ALA A 131 -170.89 -62.70 REMARK 500 VAL A 132 103.22 -179.98 REMARK 500 PRO A 138 -49.31 -27.26 REMARK 500 THR A 153 89.57 -64.51 REMARK 500 GLU A 154 150.90 -35.50 REMARK 500 HIS A 164 -10.37 -45.00 REMARK 500 SER A 166 159.35 -47.49 REMARK 500 SER A 200 178.53 -48.43 REMARK 500 ASP A 205 73.41 -106.87 REMARK 500 THR A 206 129.58 -39.58 REMARK 500 ASP A 208 87.21 -154.08 REMARK 500 GLN A 215 -14.19 -47.45 REMARK 500 ARG A 231 13.47 -60.23 REMARK 500 ASP A 247 2.27 -66.81 REMARK 500 GLN A 257 -87.33 -83.06 REMARK 500 ASP A 266 44.53 -93.22 REMARK 500 PHE A 269 73.30 -104.23 REMARK 500 GLU A 271 -92.67 -66.56 REMARK 500 PRO A 274 160.02 -40.46 REMARK 500 SER A 276 61.77 62.14 REMARK 500 SER A 279 -42.11 -143.34 REMARK 500 TYR A 283 165.02 176.12 REMARK 500 ALA A 287 -142.28 -98.77 REMARK 500 GLN A 289 40.59 178.13 REMARK 500 ALA A 292 2.18 -59.29 REMARK 500 ARG A 297 82.70 -69.03 REMARK 500 ASN A 328 13.03 -59.37 REMARK 500 LEU A 341 -80.97 -59.37 REMARK 500 ASN A 346 106.65 172.37 REMARK 500 LEU A 363 51.87 -111.09 REMARK 500 GLN A 367 -90.33 -139.26 REMARK 500 GLU A 433 -17.70 -42.95 REMARK 500 MET A 460 151.74 -45.03 REMARK 500 REMARK 500 THIS ENTRY HAS 127 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 143 OD1 REMARK 620 2 ASN A 143 ND2 44.2 REMARK 620 3 ASP A 145 O 76.8 110.0 REMARK 620 4 ASN A 148 OD1 157.3 153.7 81.1 REMARK 620 5 ASN A 148 ND2 116.1 159.1 50.7 43.0 REMARK 620 6 ASP A 149 OD2 87.8 66.3 80.2 93.4 112.0 REMARK 620 7 GLY A 169 O 80.1 54.6 156.0 121.1 139.3 105.4 REMARK 620 8 ASP A 171 OD2 65.3 99.0 80.9 106.4 72.1 150.0 83.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 143 OD1 REMARK 620 2 ASN B 143 ND2 39.3 REMARK 620 3 ASP B 145 O 43.8 77.4 REMARK 620 4 ASN B 148 OD1 102.4 130.3 58.6 REMARK 620 5 ASP B 149 OD1 68.0 63.0 58.7 74.3 REMARK 620 6 GLY B 169 O 86.8 52.9 129.6 165.4 99.3 REMARK 620 7 ASP B 171 OD1 53.2 89.7 47.7 77.8 105.5 116.7 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JI2 RELATED DB: PDB REMARK 900 RELATED ID: 1VFK RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ACARBOSE REMARK 900 RELATED ID: 1VFM RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ALPHA-CYCLODEXTRIN REMARK 900 RELATED ID: 1VFO RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH BETA-CYCLODEXTRIN DBREF 1VFU A 1 585 UNP Q08751 NEP2_THEVU 1 585 DBREF 1VFU B 1 585 UNP Q08751 NEP2_THEVU 1 585 SEQADV 1VFU ASN A 325 UNP Q08751 ASP 325 ENGINEERED MUTATION SEQADV 1VFU ASN A 421 UNP Q08751 ASP 421 ENGINEERED MUTATION SEQADV 1VFU ASN B 325 UNP Q08751 ASP 325 ENGINEERED MUTATION SEQADV 1VFU ASN B 421 UNP Q08751 ASP 421 ENGINEERED MUTATION SEQRES 1 A 585 MET LEU LEU GLU ALA ILE PHE HIS GLU ALA LYS GLY SER SEQRES 2 A 585 TYR ALA TYR PRO ILE SER GLU THR GLN LEU ARG VAL ARG SEQRES 3 A 585 LEU ARG ALA LYS LYS GLY ASP VAL VAL ARG CYS GLU VAL SEQRES 4 A 585 LEU TYR ALA ASP ARG TYR ALA SER PRO GLU GLU GLU LEU SEQRES 5 A 585 ALA HIS ALA LEU ALA GLY LYS ALA GLY SER ASP GLU ARG SEQRES 6 A 585 PHE ASP TYR PHE GLU ALA LEU LEU GLU CYS SER THR LYS SEQRES 7 A 585 ARG VAL LYS TYR VAL PHE LEU LEU THR GLY PRO GLN GLY SEQRES 8 A 585 GLU ALA VAL TYR PHE GLY GLU THR GLY PHE SER ALA GLU SEQRES 9 A 585 ARG SER LYS ALA GLY VAL PHE GLN TYR ALA TYR ILE HIS SEQRES 10 A 585 ARG SER GLU VAL PHE THR THR PRO GLU TRP ALA LYS GLU SEQRES 11 A 585 ALA VAL ILE TYR GLN ILE PHE PRO GLU ARG PHE ALA ASN SEQRES 12 A 585 GLY ASP PRO SER ASN ASP PRO PRO GLY THR GLU GLN TRP SEQRES 13 A 585 ALA LYS ASP ALA ARG PRO ARG HIS ASP SER PHE TYR GLY SEQRES 14 A 585 GLY ASP LEU LYS GLY VAL ILE ASP ARG LEU PRO TYR LEU SEQRES 15 A 585 GLU GLU LEU GLY VAL THR ALA LEU TYR PHE THR PRO ILE SEQRES 16 A 585 PHE ALA SER PRO SER HIS HIS LYS TYR ASP THR ALA ASP SEQRES 17 A 585 TYR LEU ALA ILE ASP PRO GLN PHE GLY ASP LEU PRO THR SEQRES 18 A 585 PHE ARG ARG LEU VAL ASP GLU ALA HIS ARG ARG GLY ILE SEQRES 19 A 585 LYS ILE ILE LEU ASP ALA VAL PHE ASN HIS ALA GLY ASP SEQRES 20 A 585 GLN PHE PHE ALA PHE ARG ASP VAL LEU GLN LYS GLY GLU SEQRES 21 A 585 GLN SER ARG TYR LYS ASP TRP PHE PHE ILE GLU ASP PHE SEQRES 22 A 585 PRO VAL SER LYS THR SER ARG THR ASN TYR GLU THR PHE SEQRES 23 A 585 ALA VAL GLN VAL PRO ALA MET PRO LYS LEU ARG THR GLU SEQRES 24 A 585 ASN PRO GLU VAL LYS GLU TYR LEU PHE ASP VAL ALA ARG SEQRES 25 A 585 PHE TRP MET GLU GLN GLY ILE ASP GLY TRP ARG LEU ASN SEQRES 26 A 585 VAL ALA ASN GLU VAL ASP HIS ALA PHE TRP ARG GLU PHE SEQRES 27 A 585 ARG ARG LEU VAL LYS SER LEU ASN PRO ASP ALA LEU ILE SEQRES 28 A 585 VAL GLY GLU ILE TRP HIS ASP ALA SER GLY TRP LEU MET SEQRES 29 A 585 GLY ASP GLN PHE ASP SER VAL MET ASN TYR LEU PHE ARG SEQRES 30 A 585 GLU SER VAL ILE ARG PHE PHE ALA THR GLY GLU ILE HIS SEQRES 31 A 585 ALA GLU ARG PHE ASP ALA GLU LEU THR ARG ALA ARG MET SEQRES 32 A 585 LEU TYR PRO GLU GLN ALA ALA GLN GLY LEU TRP ASN LEU SEQRES 33 A 585 LEU ASP SER HIS ASN THR GLU ARG PHE LEU THR SER CYS SEQRES 34 A 585 GLY GLY ASN GLU ALA LYS PHE ARG LEU ALA VAL LEU PHE SEQRES 35 A 585 GLN MET THR TYR LEU GLY THR PRO LEU ILE TYR TYR GLY SEQRES 36 A 585 ASP GLU ILE GLY MET ALA GLY ALA THR ASP PRO ASP CYS SEQRES 37 A 585 ARG ARG PRO MET ILE TRP GLU GLU LYS GLU GLN ASN ARG SEQRES 38 A 585 GLY LEU PHE GLU PHE TYR LYS GLU LEU ILE ARG LEU ARG SEQRES 39 A 585 HIS ARG LEU ALA SER LEU THR ARG GLY ASN VAL ARG SER SEQRES 40 A 585 TRP HIS ALA ASP LYS GLN ALA ASN LEU TYR ALA PHE VAL SEQRES 41 A 585 ARG THR VAL GLN ASP GLN HIS VAL GLY VAL VAL LEU ASN SEQRES 42 A 585 ASN ARG GLY GLU LYS GLN THR VAL LEU LEU GLN VAL PRO SEQRES 43 A 585 GLU SER GLY GLY LYS THR TRP LEU ASP CYS LEU THR GLY SEQRES 44 A 585 GLU GLU VAL HIS GLY LYS GLN GLY GLN LEU LYS LEU THR SEQRES 45 A 585 LEU ARG PRO TYR GLN GLY MET ILE LEU TRP ASN GLY ARG SEQRES 1 B 585 MET LEU LEU GLU ALA ILE PHE HIS GLU ALA LYS GLY SER SEQRES 2 B 585 TYR ALA TYR PRO ILE SER GLU THR GLN LEU ARG VAL ARG SEQRES 3 B 585 LEU ARG ALA LYS LYS GLY ASP VAL VAL ARG CYS GLU VAL SEQRES 4 B 585 LEU TYR ALA ASP ARG TYR ALA SER PRO GLU GLU GLU LEU SEQRES 5 B 585 ALA HIS ALA LEU ALA GLY LYS ALA GLY SER ASP GLU ARG SEQRES 6 B 585 PHE ASP TYR PHE GLU ALA LEU LEU GLU CYS SER THR LYS SEQRES 7 B 585 ARG VAL LYS TYR VAL PHE LEU LEU THR GLY PRO GLN GLY SEQRES 8 B 585 GLU ALA VAL TYR PHE GLY GLU THR GLY PHE SER ALA GLU SEQRES 9 B 585 ARG SER LYS ALA GLY VAL PHE GLN TYR ALA TYR ILE HIS SEQRES 10 B 585 ARG SER GLU VAL PHE THR THR PRO GLU TRP ALA LYS GLU SEQRES 11 B 585 ALA VAL ILE TYR GLN ILE PHE PRO GLU ARG PHE ALA ASN SEQRES 12 B 585 GLY ASP PRO SER ASN ASP PRO PRO GLY THR GLU GLN TRP SEQRES 13 B 585 ALA LYS ASP ALA ARG PRO ARG HIS ASP SER PHE TYR GLY SEQRES 14 B 585 GLY ASP LEU LYS GLY VAL ILE ASP ARG LEU PRO TYR LEU SEQRES 15 B 585 GLU GLU LEU GLY VAL THR ALA LEU TYR PHE THR PRO ILE SEQRES 16 B 585 PHE ALA SER PRO SER HIS HIS LYS TYR ASP THR ALA ASP SEQRES 17 B 585 TYR LEU ALA ILE ASP PRO GLN PHE GLY ASP LEU PRO THR SEQRES 18 B 585 PHE ARG ARG LEU VAL ASP GLU ALA HIS ARG ARG GLY ILE SEQRES 19 B 585 LYS ILE ILE LEU ASP ALA VAL PHE ASN HIS ALA GLY ASP SEQRES 20 B 585 GLN PHE PHE ALA PHE ARG ASP VAL LEU GLN LYS GLY GLU SEQRES 21 B 585 GLN SER ARG TYR LYS ASP TRP PHE PHE ILE GLU ASP PHE SEQRES 22 B 585 PRO VAL SER LYS THR SER ARG THR ASN TYR GLU THR PHE SEQRES 23 B 585 ALA VAL GLN VAL PRO ALA MET PRO LYS LEU ARG THR GLU SEQRES 24 B 585 ASN PRO GLU VAL LYS GLU TYR LEU PHE ASP VAL ALA ARG SEQRES 25 B 585 PHE TRP MET GLU GLN GLY ILE ASP GLY TRP ARG LEU ASN SEQRES 26 B 585 VAL ALA ASN GLU VAL ASP HIS ALA PHE TRP ARG GLU PHE SEQRES 27 B 585 ARG ARG LEU VAL LYS SER LEU ASN PRO ASP ALA LEU ILE SEQRES 28 B 585 VAL GLY GLU ILE TRP HIS ASP ALA SER GLY TRP LEU MET SEQRES 29 B 585 GLY ASP GLN PHE ASP SER VAL MET ASN TYR LEU PHE ARG SEQRES 30 B 585 GLU SER VAL ILE ARG PHE PHE ALA THR GLY GLU ILE HIS SEQRES 31 B 585 ALA GLU ARG PHE ASP ALA GLU LEU THR ARG ALA ARG MET SEQRES 32 B 585 LEU TYR PRO GLU GLN ALA ALA GLN GLY LEU TRP ASN LEU SEQRES 33 B 585 LEU ASP SER HIS ASN THR GLU ARG PHE LEU THR SER CYS SEQRES 34 B 585 GLY GLY ASN GLU ALA LYS PHE ARG LEU ALA VAL LEU PHE SEQRES 35 B 585 GLN MET THR TYR LEU GLY THR PRO LEU ILE TYR TYR GLY SEQRES 36 B 585 ASP GLU ILE GLY MET ALA GLY ALA THR ASP PRO ASP CYS SEQRES 37 B 585 ARG ARG PRO MET ILE TRP GLU GLU LYS GLU GLN ASN ARG SEQRES 38 B 585 GLY LEU PHE GLU PHE TYR LYS GLU LEU ILE ARG LEU ARG SEQRES 39 B 585 HIS ARG LEU ALA SER LEU THR ARG GLY ASN VAL ARG SER SEQRES 40 B 585 TRP HIS ALA ASP LYS GLN ALA ASN LEU TYR ALA PHE VAL SEQRES 41 B 585 ARG THR VAL GLN ASP GLN HIS VAL GLY VAL VAL LEU ASN SEQRES 42 B 585 ASN ARG GLY GLU LYS GLN THR VAL LEU LEU GLN VAL PRO SEQRES 43 B 585 GLU SER GLY GLY LYS THR TRP LEU ASP CYS LEU THR GLY SEQRES 44 B 585 GLU GLU VAL HIS GLY LYS GLN GLY GLN LEU LYS LEU THR SEQRES 45 B 585 LEU ARG PRO TYR GLN GLY MET ILE LEU TRP ASN GLY ARG HET GLC C 1 11 HET GLC C 2 11 HET GLC C 3 11 HET GLC C 4 11 HET GLC C 5 11 HET GLC C 6 11 HET GLC C 7 11 HET GLC C 8 11 HET GLC D 1 11 HET GLC D 2 11 HET GLC D 3 11 HET GLC D 4 11 HET GLC D 5 11 HET GLC D 6 11 HET GLC D 7 11 HET GLC D 8 11 HET CA A1001 1 HET CA B1002 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 GLC 16(C6 H12 O6) FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *133(H2 O) HELIX 1 1 LEU A 2 ILE A 6 5 5 HELIX 2 2 GLU A 104 GLY A 109 1 6 HELIX 3 3 HIS A 117 VAL A 121 5 5 HELIX 4 4 PRO A 125 GLU A 130 1 6 HELIX 5 5 PHE A 137 ALA A 142 1 6 HELIX 6 6 ASP A 171 ARG A 178 1 8 HELIX 7 7 ARG A 178 GLY A 186 1 9 HELIX 8 8 PRO A 214 GLY A 217 5 4 HELIX 9 9 ASP A 218 ARG A 231 1 14 HELIX 10 10 PHE A 249 LYS A 258 1 10 HELIX 11 11 GLY A 259 SER A 262 5 4 HELIX 12 12 TYR A 264 PHE A 268 5 5 HELIX 13 13 ASN A 300 GLN A 317 1 18 HELIX 14 14 VAL A 326 VAL A 330 5 5 HELIX 15 15 ASP A 331 LEU A 345 1 15 HELIX 16 16 ALA A 359 LEU A 363 5 5 HELIX 17 17 ASN A 373 ALA A 385 1 13 HELIX 18 18 HIS A 390 MET A 403 1 14 HELIX 19 19 PRO A 406 GLN A 411 1 6 HELIX 20 20 ARG A 424 CYS A 429 1 6 HELIX 21 21 ASN A 432 MET A 444 1 13 HELIX 22 22 GLY A 455 GLY A 459 5 5 HELIX 23 23 GLU A 475 GLN A 479 5 5 HELIX 24 24 ASN A 480 LEU A 497 1 18 HELIX 25 25 LEU A 497 GLY A 503 1 7 HELIX 26 26 LEU B 2 ILE B 6 5 5 HELIX 27 27 ARG B 105 GLY B 109 5 5 HELIX 28 28 HIS B 117 VAL B 121 5 5 HELIX 29 29 GLU B 126 ALA B 131 5 6 HELIX 30 30 PHE B 137 ALA B 142 1 6 HELIX 31 31 ASP B 171 GLY B 186 1 16 HELIX 32 32 ASP B 213 GLY B 217 5 5 HELIX 33 33 ASP B 218 ARG B 231 1 14 HELIX 34 34 PHE B 249 GLN B 257 1 9 HELIX 35 35 ASN B 300 GLY B 318 1 19 HELIX 36 36 VAL B 326 VAL B 330 5 5 HELIX 37 37 ASP B 331 ASN B 346 1 16 HELIX 38 38 ASN B 373 PHE B 384 1 12 HELIX 39 39 HIS B 390 MET B 403 1 14 HELIX 40 40 PRO B 406 LEU B 413 1 8 HELIX 41 41 ARG B 424 CYS B 429 1 6 HELIX 42 42 ASN B 432 MET B 444 1 13 HELIX 43 43 GLY B 455 GLY B 459 5 5 HELIX 44 44 ASN B 480 LEU B 497 1 18 HELIX 45 45 LEU B 497 GLY B 503 1 7 SHEET 1 A 4 ALA A 15 PRO A 17 0 SHEET 2 A 4 GLN A 22 LYS A 30 -1 O ARG A 24 N TYR A 16 SHEET 3 A 4 PHE A 66 GLU A 74 -1 O PHE A 69 N LEU A 27 SHEET 4 A 4 GLY A 58 SER A 62 -1 N GLY A 61 O TYR A 68 SHEET 1 B 4 ARG A 36 ALA A 42 0 SHEET 2 B 4 VAL A 80 THR A 87 -1 O THR A 87 N ARG A 36 SHEET 3 B 4 TYR A 95 GLY A 97 -1 O PHE A 96 N PHE A 84 SHEET 4 B 4 GLY A 100 SER A 102 -1 O SER A 102 N TYR A 95 SHEET 1 C 3 ARG A 36 ALA A 42 0 SHEET 2 C 3 VAL A 80 THR A 87 -1 O THR A 87 N ARG A 36 SHEET 3 C 3 PHE A 111 TYR A 113 -1 O TYR A 113 N VAL A 80 SHEET 1 D 8 SER A 370 VAL A 371 0 SHEET 2 D 8 LEU A 350 GLY A 353 1 N GLY A 353 O SER A 370 SHEET 3 D 8 GLY A 321 LEU A 324 1 N LEU A 324 O VAL A 352 SHEET 4 D 8 LYS A 235 ALA A 240 1 N LEU A 238 O ARG A 323 SHEET 5 D 8 ALA A 189 PHE A 192 1 N PHE A 192 O ILE A 237 SHEET 6 D 8 ILE A 133 ILE A 136 1 N ILE A 136 O TYR A 191 SHEET 7 D 8 THR A 449 TYR A 453 1 O ILE A 452 N ILE A 133 SHEET 8 D 8 TRP A 414 LEU A 416 1 N ASN A 415 O THR A 449 SHEET 1 E 2 PHE A 196 ALA A 197 0 SHEET 2 E 2 ASP A 208 ILE A 212 -1 O ALA A 211 N ALA A 197 SHEET 1 F 6 SER A 507 ASP A 511 0 SHEET 2 F 6 LEU A 516 THR A 522 -1 O ALA A 518 N TRP A 508 SHEET 3 F 6 HIS A 527 ASN A 533 -1 O LEU A 532 N TYR A 517 SHEET 4 F 6 GLY A 578 TRP A 582 -1 O LEU A 581 N GLY A 529 SHEET 5 F 6 THR A 552 ASP A 555 -1 N LEU A 554 O TRP A 582 SHEET 6 F 6 GLU A 561 HIS A 563 -1 O VAL A 562 N TRP A 553 SHEET 1 G 2 GLN A 539 GLN A 544 0 SHEET 2 G 2 GLN A 568 LEU A 573 -1 O LEU A 571 N VAL A 541 SHEET 1 H 8 ALA B 15 PRO B 17 0 SHEET 2 H 8 GLN B 22 LYS B 30 -1 O ARG B 24 N TYR B 16 SHEET 3 H 8 PHE B 66 GLU B 74 -1 O PHE B 69 N LEU B 27 SHEET 4 H 8 ALA B 53 SER B 62 -1 N ALA B 60 O TYR B 68 SHEET 5 H 8 ARG B 36 ALA B 42 -1 N TYR B 41 O ALA B 53 SHEET 6 H 8 VAL B 80 THR B 87 -1 O LEU B 85 N GLU B 38 SHEET 7 H 8 ALA B 93 PHE B 96 -1 O VAL B 94 N LEU B 86 SHEET 8 H 8 PHE B 101 SER B 102 -1 O SER B 102 N TYR B 95 SHEET 1 I 7 ALA B 15 PRO B 17 0 SHEET 2 I 7 GLN B 22 LYS B 30 -1 O ARG B 24 N TYR B 16 SHEET 3 I 7 PHE B 66 GLU B 74 -1 O PHE B 69 N LEU B 27 SHEET 4 I 7 ALA B 53 SER B 62 -1 N ALA B 60 O TYR B 68 SHEET 5 I 7 ARG B 36 ALA B 42 -1 N TYR B 41 O ALA B 53 SHEET 6 I 7 VAL B 80 THR B 87 -1 O LEU B 85 N GLU B 38 SHEET 7 I 7 PHE B 111 TYR B 113 -1 O TYR B 113 N VAL B 80 SHEET 1 J 8 SER B 370 VAL B 371 0 SHEET 2 J 8 LEU B 350 GLY B 353 1 N GLY B 353 O SER B 370 SHEET 3 J 8 GLY B 321 ASN B 325 1 N LEU B 324 O VAL B 352 SHEET 4 J 8 LYS B 235 VAL B 241 1 N ALA B 240 O ASN B 325 SHEET 5 J 8 ALA B 189 PHE B 192 1 N LEU B 190 O ILE B 237 SHEET 6 J 8 ILE B 133 ILE B 136 1 N TYR B 134 O TYR B 191 SHEET 7 J 8 THR B 449 TYR B 453 1 O ILE B 452 N ILE B 133 SHEET 8 J 8 TRP B 414 ASN B 415 1 N ASN B 415 O THR B 449 SHEET 1 K 6 SER B 507 ASP B 511 0 SHEET 2 K 6 LEU B 516 VAL B 523 -1 O ALA B 518 N TRP B 508 SHEET 3 K 6 GLN B 526 ASN B 533 -1 O LEU B 532 N TYR B 517 SHEET 4 K 6 MET B 579 TRP B 582 -1 O MET B 579 N VAL B 531 SHEET 5 K 6 THR B 552 ASP B 555 -1 N LEU B 554 O TRP B 582 SHEET 6 K 6 GLU B 561 HIS B 563 -1 O VAL B 562 N TRP B 553 SHEET 1 L 2 GLN B 539 GLN B 544 0 SHEET 2 L 2 GLN B 568 LEU B 573 -1 O LEU B 571 N VAL B 541 LINK O4 GLC C 1 C1 GLC C 2 1555 1555 1.40 LINK C1 GLC C 1 O4 GLC C 8 1555 1555 1.40 LINK O4 GLC C 2 C1 GLC C 3 1555 1555 1.40 LINK O4 GLC C 3 C1 GLC C 4 1555 1555 1.40 LINK O4 GLC C 4 C1 GLC C 5 1555 1555 1.40 LINK O4 GLC C 5 C1 GLC C 6 1555 1555 1.40 LINK O4 GLC C 6 C1 GLC C 7 1555 1555 1.41 LINK O4 GLC C 7 C1 GLC C 8 1555 1555 1.40 LINK O4 GLC D 1 C1 GLC D 2 1555 1555 1.40 LINK C1 GLC D 1 O4 GLC D 8 1555 1555 1.41 LINK O4 GLC D 2 C1 GLC D 3 1555 1555 1.40 LINK O4 GLC D 3 C1 GLC D 4 1555 1555 1.41 LINK O4 GLC D 4 C1 GLC D 5 1555 1555 1.41 LINK O4 GLC D 5 C1 GLC D 6 1555 1555 1.41 LINK O4 GLC D 6 C1 GLC D 7 1555 1555 1.40 LINK O4 GLC D 7 C1 GLC D 8 1555 1555 1.41 LINK OD1 ASN A 143 CA CA A1001 1555 1555 2.70 LINK ND2 ASN A 143 CA CA A1001 1555 1555 3.15 LINK O ASP A 145 CA CA A1001 1555 1555 2.83 LINK OD1 ASN A 148 CA CA A1001 1555 1555 2.24 LINK ND2 ASN A 148 CA CA A1001 1555 1555 3.28 LINK OD2 ASP A 149 CA CA A1001 1555 1555 2.44 LINK O GLY A 169 CA CA A1001 1555 1555 2.39 LINK OD2 ASP A 171 CA CA A1001 1555 1555 2.38 LINK OD1 ASN B 143 CA CA B1002 1555 1555 3.55 LINK ND2 ASN B 143 CA CA B1002 1555 1555 2.79 LINK O ASP B 145 CA CA B1002 1555 1555 3.20 LINK OD1 ASN B 148 CA CA B1002 1555 1555 2.12 LINK OD1 ASP B 149 CA CA B1002 1555 1555 3.10 LINK O GLY B 169 CA CA B1002 1555 1555 2.55 LINK OD1 ASP B 171 CA CA B1002 1555 1555 3.21 CISPEP 1 PHE A 273 PRO A 274 0 1.02 CISPEP 2 ASP A 465 PRO A 466 0 0.54 CISPEP 3 PHE B 273 PRO B 274 0 -0.29 CISPEP 4 ASP B 465 PRO B 466 0 0.01 CRYST1 113.454 118.496 114.080 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 0.008814 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008766 0.00000