PDB Short entry for 2JFE HEADER HYDROLASE 31-JAN-07 2JFE TITLE THE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BETA-GLUCOSIDASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSOLIC BETA-GLUCOSIDASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: HUMAN CYTOSOLIC BETA-GLUCOSIDASE; COMPND 5 EC: 3.2.1.21; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL: CYTOSOLIC; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: (HIS4)/GS115; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PHIL-S1; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIL-S1/CBG-1 KEYWDS HYDROLASE, HUMAN CYTOSOLIC BETA-GLUCOSIDASE, FAMILY GH1 BETA- KEYWDS 2 GLUCOSIDASE, ALTERNATIVE SPLICING, FLAVONOID-GLYCOSIDASE, KEYWDS 3 GLYCOSIDASE, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR M.CZJZEK,S.TRIBOLO,J.G.BERRIN,P.A.KROON,N.JUGE REVDAT 5 13-DEC-23 2JFE 1 HETSYN REVDAT 4 29-JUL-20 2JFE 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 24-FEB-09 2JFE 1 VERSN REVDAT 2 26-JUN-07 2JFE 1 JRNL REVDAT 1 19-JUN-07 2JFE 0 JRNL AUTH S.TRIBOLO,J.G.BERRIN,P.A.KROON,M.CZJZEK,N.JUGE JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BETA-GLUCOSIDASE JRNL TITL 2 UNRAVELS THE SUBSTRATE AGLYCONE SPECIFICITY OF A FAMILY 1 JRNL TITL 3 GLYCOSIDE HYDROLASE JRNL REF J.MOL.BIOL. V. 370 964 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17555766 JRNL DOI 10.1016/J.JMB.2007.05.034 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 16273 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 + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 865 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1170 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1660 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3725 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.42000 REMARK 3 B22 (A**2) : 1.42000 REMARK 3 B33 (A**2) : -2.13000 REMARK 3 B12 (A**2) : 0.71000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.355 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.377 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.142 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.378 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.858 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3871 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5264 ; 1.632 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 458 ; 8.956 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 191 ;37.192 ;24.346 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 613 ;19.646 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.547 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3009 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2168 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2642 ; 0.318 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 210 ; 0.210 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 35 ; 0.249 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.261 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2337 ; 0.618 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3686 ; 1.097 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1798 ; 1.522 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1578 ; 2.336 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2JFE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1290031306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17144 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1V02 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS GREW WITHIN SEVERAL DAYS IN REMARK 280 THE CRYSTALLIZATION TRIAL CONTAINING 0.2 M AMMONIUM SULPHATE, REMARK 280 MES BUFFER AT PH 6.5 AND 30 % (W/V) POLYETHYLENEGLYCOL- REMARK 280 MONOMETHYLETHER (PEG-MME) 5500, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.64167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.28333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.28333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 42.64167 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET X 1 REMARK 465 ALA X 2 REMARK 465 ASN X 462 REMARK 465 ASN X 463 REMARK 465 GLY X 464 REMARK 465 LEU X 465 REMARK 465 GLU X 466 REMARK 465 ALA X 467 REMARK 465 HIS X 468 REMARK 465 LEU X 469 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 PHE X 3 CG CD1 CD2 CE1 CE2 CZ 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 MET X 275 CB LYS X 278 1.91 REMARK 500 O ASP X 175 O PRO X 184 2.03 REMARK 500 O GLY X 325 N LEU X 327 2.10 REMARK 500 O ASN X 342 O ILE X 346 2.11 REMARK 500 O GLY X 322 O HOH X 2118 2.12 REMARK 500 O HOH X 2080 O HOH X 2120 2.12 REMARK 500 O ASP X 442 O ALA X 444 2.13 REMARK 500 O LYS X 256 O ILE X 260 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH X 2141 O HOH X 2141 6765 2.15 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 LEU X 253 CA - CB - CG ANGL. DEV. = 17.3 DEGREES REMARK 500 PRO X 381 C - N - CA ANGL. DEV. = 12.9 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 PRO X 4 -148.19 -94.51 REMARK 500 ALA X 5 -138.92 23.96 REMARK 500 LYS X 45 17.41 51.25 REMARK 500 ALA X 52 -126.41 43.21 REMARK 500 ASP X 122 47.17 -143.11 REMARK 500 GLU X 165 66.00 36.57 REMARK 500 SER X 221 -146.63 -146.39 REMARK 500 ALA X 232 -71.16 -44.20 REMARK 500 ASN X 235 5.60 38.76 REMARK 500 ASP X 261 -14.37 52.97 REMARK 500 LYS X 278 -108.42 21.89 REMARK 500 SER X 284 155.08 -49.70 REMARK 500 TYR X 309 -32.05 -142.16 REMARK 500 LYS X 321 97.93 65.88 REMARK 500 ILE X 326 20.20 25.58 REMARK 500 LEU X 327 -22.85 54.40 REMARK 500 ASP X 329 10.88 -65.70 REMARK 500 ALA X 330 24.42 -74.13 REMARK 500 SER X 339 50.99 -101.42 REMARK 500 ASN X 342 -71.21 -123.25 REMARK 500 VAL X 343 96.63 50.06 REMARK 500 ASP X 344 -117.56 49.32 REMARK 500 VAL X 348 85.84 -64.42 REMARK 500 PRO X 381 130.43 16.92 REMARK 500 ALA X 382 -3.04 179.96 REMARK 500 PRO X 383 -148.61 -105.89 REMARK 500 LEU X 384 -80.19 56.64 REMARK 500 SER X 418 123.61 146.43 REMARK 500 GLU X 424 59.44 -90.96 REMARK 500 TRP X 425 -126.06 55.48 REMARK 500 ALA X 444 -175.93 -62.37 REMARK 500 ILE X 460 79.13 -64.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN X 277 LYS X 278 139.45 REMARK 500 ASP X 329 ALA X 330 146.75 REMARK 500 ASP X 380 PRO X 381 -133.08 REMARK 500 ALA X 382 PRO X 383 -140.85 REMARK 500 TRP X 417 SER X 418 120.23 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 X2005 DISTANCE = 6.68 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. DBREF 2JFE X 1 469 UNP Q9H227 GBA3_HUMAN 1 469 SEQADV 2JFE ILE X 341 UNP Q9H227 LYS 341 CONFLICT SEQRES 1 X 469 MET ALA PHE PRO ALA GLY PHE GLY TRP ALA ALA ALA THR SEQRES 2 X 469 ALA ALA TYR GLN VAL GLU GLY GLY TRP ASP ALA ASP GLY SEQRES 3 X 469 LYS GLY PRO CYS VAL TRP ASP THR PHE THR HIS GLN GLY SEQRES 4 X 469 GLY GLU ARG VAL PHE LYS ASN GLN THR GLY ASP VAL ALA SEQRES 5 X 469 CYS GLY SER TYR THR LEU TRP GLU GLU ASP LEU LYS CYS SEQRES 6 X 469 ILE LYS GLN LEU GLY LEU THR HIS TYR ARG PHE SER LEU SEQRES 7 X 469 SER TRP SER ARG LEU LEU PRO ASP GLY THR THR GLY PHE SEQRES 8 X 469 ILE ASN GLN LYS GLY ILE ASP TYR TYR ASN LYS ILE ILE SEQRES 9 X 469 ASP ASP LEU LEU LYS ASN GLY VAL THR PRO ILE VAL THR SEQRES 10 X 469 LEU TYR HIS PHE ASP LEU PRO GLN THR LEU GLU ASP GLN SEQRES 11 X 469 GLY GLY TRP LEU SER GLU ALA ILE ILE GLU SER PHE ASP SEQRES 12 X 469 LYS TYR ALA GLN PHE CYS PHE SER THR PHE GLY ASP ARG SEQRES 13 X 469 VAL LYS GLN TRP ILE THR ILE ASN GLU ALA ASN VAL LEU SEQRES 14 X 469 SER VAL MET SER TYR ASP LEU GLY MET PHE PRO PRO GLY SEQRES 15 X 469 ILE PRO HIS PHE GLY THR GLY GLY TYR GLN ALA ALA HIS SEQRES 16 X 469 ASN LEU ILE LYS ALA HIS ALA ARG SER TRP HIS SER TYR SEQRES 17 X 469 ASP SER LEU PHE ARG LYS LYS GLN LYS GLY MET VAL SER SEQRES 18 X 469 LEU SER LEU PHE ALA VAL TRP LEU GLU PRO ALA ASP PRO SEQRES 19 X 469 ASN SER VAL SER ASP GLN GLU ALA ALA LYS ARG ALA ILE SEQRES 20 X 469 THR PHE HIS LEU ASP LEU PHE ALA LYS PRO ILE PHE ILE SEQRES 21 X 469 ASP GLY ASP TYR PRO GLU VAL VAL LYS SER GLN ILE ALA SEQRES 22 X 469 SER MET SER GLN LYS GLN GLY TYR PRO SER SER ARG LEU SEQRES 23 X 469 PRO GLU PHE THR GLU GLU GLU LYS LYS MET ILE LYS GLY SEQRES 24 X 469 THR ALA ASP PHE PHE ALA VAL GLN TYR TYR THR THR ARG SEQRES 25 X 469 LEU ILE LYS TYR GLN GLU ASN LYS LYS GLY GLU LEU GLY SEQRES 26 X 469 ILE LEU GLN ASP ALA GLU ILE GLU PHE PHE PRO ASP PRO SEQRES 27 X 469 SER TRP ILE ASN VAL ASP TRP ILE TYR VAL VAL PRO TRP SEQRES 28 X 469 GLY VAL CYS LYS LEU LEU LYS TYR ILE LYS ASP THR TYR SEQRES 29 X 469 ASN ASN PRO VAL ILE TYR ILE THR GLU ASN GLY PHE PRO SEQRES 30 X 469 GLN SER ASP PRO ALA PRO LEU ASP ASP THR GLN ARG TRP SEQRES 31 X 469 GLU TYR PHE ARG GLN THR PHE GLN GLU LEU PHE LYS ALA SEQRES 32 X 469 ILE GLN LEU ASP LYS VAL ASN LEU GLN VAL TYR CYS ALA SEQRES 33 X 469 TRP SER LEU LEU ASP ASN PHE GLU TRP ASN GLN GLY TYR SEQRES 34 X 469 SER SER ARG PHE GLY LEU PHE HIS VAL ASP PHE GLU ASP SEQRES 35 X 469 PRO ALA ARG PRO ARG VAL PRO TYR THR SER ALA LYS GLU SEQRES 36 X 469 TYR ALA LYS ILE ILE ARG ASN ASN GLY LEU GLU ALA HIS SEQRES 37 X 469 LEU MODRES 2JFE ASN X 46 ASN GLYCOSYLATION SITE HET NAG A 1 14 HET NAG A 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 3 HOH *158(H2 O) HELIX 1 1 ALA X 14 GLU X 19 1 6 HELIX 2 2 CYS X 30 GLN X 38 1 9 HELIX 3 3 VAL X 43 GLN X 47 5 5 HELIX 4 4 LEU X 58 GLY X 70 1 13 HELIX 5 5 SER X 79 LEU X 84 1 6 HELIX 6 6 ASN X 93 ASN X 110 1 18 HELIX 7 7 PRO X 124 GLN X 130 1 7 HELIX 8 8 GLY X 131 SER X 135 5 5 HELIX 9 9 GLU X 136 GLY X 154 1 19 HELIX 10 10 GLU X 165 TYR X 174 1 10 HELIX 11 11 THR X 188 PHE X 212 1 25 HELIX 12 12 PHE X 212 LYS X 217 1 6 HELIX 13 13 SER X 236 LEU X 251 1 16 HELIX 14 14 LEU X 251 ILE X 260 1 10 HELIX 15 15 PRO X 265 LYS X 278 1 14 HELIX 16 16 THR X 290 LYS X 298 1 9 HELIX 17 17 PRO X 350 TYR X 364 1 15 HELIX 18 18 ASP X 386 LEU X 406 1 21 HELIX 19 19 GLU X 424 TYR X 429 5 6 HELIX 20 20 TYR X 450 ILE X 460 1 11 SHEET 1 XA 9 MET X 219 SER X 221 0 SHEET 2 XA 9 GLN X 159 ILE X 163 1 O TRP X 160 N SER X 221 SHEET 3 XA 9 THR X 113 TYR X 119 1 O VAL X 116 N ILE X 161 SHEET 4 XA 9 HIS X 73 SER X 77 1 O TYR X 74 N ILE X 115 SHEET 5 XA 9 GLY X 8 ALA X 12 1 O ALA X 11 N ARG X 75 SHEET 6 XA 9 LEU X 411 ALA X 416 1 O GLN X 412 N GLY X 8 SHEET 7 XA 9 ILE X 369 ASN X 374 1 O ILE X 369 N GLN X 412 SHEET 8 XA 9 PHE X 304 TYR X 316 1 O PHE X 304 N TYR X 370 SHEET 9 XA 9 SER X 223 PRO X 231 1 O LEU X 224 N GLN X 307 SHEET 1 XB 9 MET X 219 SER X 221 0 SHEET 2 XB 9 GLN X 159 ILE X 163 1 O TRP X 160 N SER X 221 SHEET 3 XB 9 THR X 113 TYR X 119 1 O VAL X 116 N ILE X 161 SHEET 4 XB 9 HIS X 73 SER X 77 1 O TYR X 74 N ILE X 115 SHEET 5 XB 9 GLY X 8 ALA X 12 1 O ALA X 11 N ARG X 75 SHEET 6 XB 9 LEU X 411 ALA X 416 1 O GLN X 412 N GLY X 8 SHEET 7 XB 9 ILE X 369 ASN X 374 1 O ILE X 369 N GLN X 412 SHEET 8 XB 9 PHE X 304 TYR X 316 1 O PHE X 304 N TYR X 370 SHEET 9 XB 9 ILE X 332 PHE X 335 -1 O GLU X 333 N LYS X 315 SHEET 1 XC 2 GLN X 378 SER X 379 0 SHEET 2 XC 2 SER X 431 ARG X 432 -1 O ARG X 432 N GLN X 378 SHEET 1 XD 2 PHE X 436 VAL X 438 0 SHEET 2 XD 2 ARG X 447 PRO X 449 -1 O VAL X 448 N HIS X 437 LINK ND2 ASN X 46 C1 NAG A 1 1555 1555 1.45 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 CISPEP 1 PRO X 180 PRO X 181 0 1.68 CRYST1 90.479 90.479 127.925 90.00 90.00 120.00 P 31 2 1 6 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 0.011052 0.006381 0.000000 0.00000 SCALE2 0.000000 0.012762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007817 0.00000