HEADER HYDROLASE 04-JUL-24 9FZ3 TITLE CRYSTAL STRUCTURE OF K38 AMYLASE FROM BACILLUS SP. STRAIN KSM-K38 TITLE 2 COVALENTLY BOUND TO ALPHA-1,6 BRANCHED PSEUDO-TRISACCHARIDE ACTIVITY- TITLE 3 BASED PROBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SP. KSM-K38; SOURCE 3 ORGANISM_TAXID: 129736; SOURCE 4 GENE: AMYK38; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSIDE HYDROLASE, AMYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR I.B.PICKLES,O.MOROZ,G.DAVIES REVDAT 1 11-DEC-24 9FZ3 0 JRNL AUTH I.B.PICKLES,Y.CHEN,O.MOROZ,H.A.BROWN,C.DE BOER,Z.ARMSTRONG, JRNL AUTH 2 N.G.S.MCGREGOR,M.ARTOLA,J.D.C.CODEE,N.M.KOROPATKIN, JRNL AUTH 3 H.S.OVERKLEEFT,G.J.DAVIES JRNL TITL PRECISION ACTIVITY-BASED ALPHA-AMYLASE PROBES FOR DISSECTION JRNL TITL 2 AND ANNOTATION OF LINEAR AND BRANCHED-CHAIN STARCH-DEGRADING JRNL TITL 3 ENZYMES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. 15219 2024 JRNL REFN ESSN 1521-3773 JRNL PMID 39601378 JRNL DOI 10.1002/ANIE.202415219 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 48345 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2598 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3530 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 208 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3890 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.724 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4072 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3422 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5531 ; 1.628 ; 1.782 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7849 ; 0.581 ; 1.768 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 7.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 7.620 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 576 ;13.007 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.262 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5053 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1077 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1916 ; 4.075 ; 4.575 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1915 ; 4.066 ; 4.574 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2392 ; 5.149 ; 8.220 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2393 ; 5.150 ; 8.221 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2156 ; 4.187 ; 4.792 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2153 ; 4.187 ; 4.792 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3137 ; 5.670 ; 8.674 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4842 ; 6.928 ;47.300 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4807 ; 6.913 ;46.270 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 : 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 9FZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1292137132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51019 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 66.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 41.10 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE PH 5, 34% (W/V) PEG 4000 AND 1 MM 4'- REMARK 280 OCTYLAMINE-ALPHA-D-MALTOTRIOSE EPICYCLOPHELLITOL (COMPOUND 2A)., REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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: MONOMERIC 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 930 LIES ON A SPECIAL POSITION. 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 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 SER A 10 REMARK 465 SER A 11 REMARK 465 GLY A 12 REMARK 465 LEU A 13 REMARK 465 GLU A 14 REMARK 465 VAL A 15 REMARK 465 LEU A 16 REMARK 465 PHE A 17 REMARK 465 GLN A 18 REMARK 465 GLY A 19 REMARK 465 PRO A 20 REMARK 465 ALA A 21 REMARK 465 ASP A 22 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 LEU A 24 CG CD1 CD2 REMARK 470 ASN A 193 CG OD1 ND2 REMARK 470 GLU A 228 CG CD OE1 OE2 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 OG SER A 165 O HOH A 701 2.19 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 ARG A 106 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 252 CB - CG - OD1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP A 252 CB - CG - OD2 ANGL. DEV. = -7.0 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 TYR A 31 55.39 -101.42 REMARK 500 LEU A 85 40.18 -98.41 REMARK 500 TYR A 171 -31.08 79.85 REMARK 500 GLN A 191 72.09 47.52 REMARK 500 ASP A 287 98.65 -169.59 REMARK 500 SER A 358 60.80 -158.32 REMARK 500 ASN A 439 2.57 83.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 146 0.08 SIDE CHAIN REMARK 500 ARG A 431 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 930 DISTANCE = 6.27 ANGSTROMS REMARK 525 HOH A 931 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 932 DISTANCE = 9.37 ANGSTROMS 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 OC9 A 602 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 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 125 OD1 REMARK 620 2 ASP A 215 O 111.5 REMARK 620 3 ASP A 215 OD1 168.2 78.9 REMARK 620 4 ASN A 221 OD1 90.1 80.2 97.5 REMARK 620 5 HIS A 256 O 90.8 91.9 82.9 171.8 REMARK 620 6 HOH A 844 O 82.5 155.2 90.0 79.4 108.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 604 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 310 OD1 REMARK 620 2 VAL A 345 O 82.3 REMARK 620 3 ASP A 346 OD1 126.6 87.1 REMARK 620 4 SER A 358 O 116.0 161.7 82.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 606 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 321 O REMARK 620 2 TYR A 323 O 87.2 REMARK 620 3 TRP A 424 O 171.6 87.3 REMARK 620 4 ASP A 425 OD1 99.5 170.9 85.4 REMARK 620 5 ASN A 448 OD1 99.0 96.5 87.9 88.5 REMARK 620 6 HOH A 859 O 82.4 88.3 91.1 86.5 175.0 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9FYZ RELATED DB: PDB REMARK 900 RELATED ID: 9FZ0 RELATED DB: PDB REMARK 900 RELATED ID: 9FZ2 RELATED DB: PDB DBREF 9FZ3 A 21 501 UNP Q93I48 Q93I48_9BACI 21 501 SEQADV 9FZ3 MET A 0 UNP Q93I48 INITIATING METHIONINE SEQADV 9FZ3 GLY A 1 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 SER A 2 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 SER A 3 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 4 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 5 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 6 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 7 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 8 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 HIS A 9 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 SER A 10 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 SER A 11 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 GLY A 12 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 LEU A 13 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 GLU A 14 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 VAL A 15 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 LEU A 16 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 PHE A 17 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 GLN A 18 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 GLY A 19 UNP Q93I48 EXPRESSION TAG SEQADV 9FZ3 PRO A 20 UNP Q93I48 EXPRESSION TAG SEQRES 1 A 502 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 502 LEU GLU VAL LEU PHE GLN GLY PRO ALA ASP GLY LEU ASN SEQRES 3 A 502 GLY THR MET MET GLN TYR TYR GLU TRP HIS LEU GLU ASN SEQRES 4 A 502 ASP GLY GLN HIS TRP ASN ARG LEU HIS ASP ASP ALA ALA SEQRES 5 A 502 ALA LEU SER ASP ALA GLY ILE THR ALA ILE TRP ILE PRO SEQRES 6 A 502 PRO ALA TYR LYS GLY ASN SER GLN ALA ASP VAL GLY TYR SEQRES 7 A 502 GLY ALA TYR ASP LEU TYR ASP LEU GLY GLU PHE ASN GLN SEQRES 8 A 502 LYS GLY THR VAL ARG THR LYS TYR GLY THR LYS ALA GLN SEQRES 9 A 502 LEU GLU ARG ALA ILE GLY SER LEU LYS SER ASN ASP ILE SEQRES 10 A 502 ASN VAL TYR GLY ASP VAL VAL MET ASN HIS LYS MET GLY SEQRES 11 A 502 ALA ASP PHE THR GLU ALA VAL GLN ALA VAL GLN VAL ASN SEQRES 12 A 502 PRO THR ASN ARG TRP GLN ASP ILE SER GLY ALA TYR THR SEQRES 13 A 502 ILE ASP ALA TRP THR GLY PHE ASP PHE SER GLY ARG ASN SEQRES 14 A 502 ASN ALA TYR SER ASP PHE LYS TRP ARG TRP PHE HIS PHE SEQRES 15 A 502 ASN GLY VAL ASP TRP ASP GLN ARG TYR GLN GLU ASN HIS SEQRES 16 A 502 ILE PHE ARG PHE ALA ASN THR ASN TRP ASN TRP ARG VAL SEQRES 17 A 502 ASP GLU GLU ASN GLY ASN TYR ASP TYR LEU LEU GLY SER SEQRES 18 A 502 ASN ILE ASP PHE SER HIS PRO GLU VAL GLN ASP GLU LEU SEQRES 19 A 502 LYS ASP TRP GLY SER TRP PHE THR ASP GLU LEU ASP LEU SEQRES 20 A 502 ASP GLY TYR ARG LEU ASP ALA ILE LYS HIS ILE PRO PHE SEQRES 21 A 502 TRP TYR THR SER ASP TRP VAL ARG HIS GLN ARG ASN GLU SEQRES 22 A 502 ALA ASP GLN ASP LEU PHE VAL VAL GLY GLU TYR TRP LYS SEQRES 23 A 502 ASP ASP VAL GLY ALA LEU GLU PHE TYR LEU ASP GLU MET SEQRES 24 A 502 ASN TRP GLU MET SER LEU PHE ASP VAL PRO LEU ASN TYR SEQRES 25 A 502 ASN PHE TYR ARG ALA SER GLN GLN GLY GLY SER TYR ASP SEQRES 26 A 502 MET ARG ASN ILE LEU ARG GLY SER LEU VAL GLU ALA HIS SEQRES 27 A 502 PRO MET HIS ALA VAL THR PHE VAL ASP ASN HIS ASP THR SEQRES 28 A 502 GLN PRO GLY GLU SER LEU GLU SER TRP VAL ALA ASP TRP SEQRES 29 A 502 PHE LYS PRO LEU ALA TYR ALA THR ILE LEU THR ARG GLU SEQRES 30 A 502 GLY GLY TYR PRO ASN VAL PHE TYR GLY ASP TYR TYR GLY SEQRES 31 A 502 ILE PRO ASN ASP ASN ILE SER ALA LYS LYS ASP MET ILE SEQRES 32 A 502 ASP GLU LEU LEU ASP ALA ARG GLN ASN TYR ALA TYR GLY SEQRES 33 A 502 THR GLN HIS ASP TYR PHE ASP HIS TRP ASP VAL VAL GLY SEQRES 34 A 502 TRP THR ARG GLU GLY SER SER SER ARG PRO ASN SER GLY SEQRES 35 A 502 LEU ALA THR ILE MET SER ASN GLY PRO GLY GLY SER LYS SEQRES 36 A 502 TRP MET TYR VAL GLY ARG GLN ASN ALA GLY GLN THR TRP SEQRES 37 A 502 THR ASP LEU THR GLY ASN ASN GLY ALA SER VAL THR ILE SEQRES 38 A 502 ASN GLY ASP GLY TRP GLY GLU PHE PHE THR ASN GLY GLY SEQRES 39 A 502 SER VAL SER VAL TYR VAL ASN GLN HET GLC B 1 11 HET GLC B 2 11 HET PBW A 601 12 HET OC9 A 602 2 HET ACT A 603 4 HET NA A 604 1 HET NA A 605 1 HET NA A 606 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM PBW (1~{S},4~{S},5~{R})-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3, HETNAM 2 PBW 4,5-PENTOL HETNAM OC9 OCTAN-1-OL HETNAM ACT ACETATE ION HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 PBW C7 H14 O6 FORMUL 4 OC9 C8 H18 O FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 NA 3(NA 1+) FORMUL 9 HOH *232(H2 O) HELIX 1 AA1 GLN A 41 GLY A 57 1 17 HELIX 2 AA2 THR A 100 ASN A 114 1 15 HELIX 3 AA3 ARG A 177 PHE A 179 5 3 HELIX 4 AA4 HIS A 226 ASP A 245 1 20 HELIX 5 AA5 PRO A 258 ALA A 273 1 16 HELIX 6 AA6 ASP A 287 MET A 298 1 12 HELIX 7 AA7 ASP A 306 GLY A 320 1 15 HELIX 8 AA8 ASP A 324 ILE A 328 5 5 HELIX 9 AA9 SER A 332 HIS A 337 1 6 HELIX 10 AB1 PHE A 364 ARG A 375 1 12 HELIX 11 AB2 TYR A 384 GLY A 389 1 6 HELIX 12 AB3 ILE A 390 ASN A 394 5 5 HELIX 13 AB4 LYS A 398 TYR A 412 1 15 HELIX 14 AB5 GLY A 459 ALA A 463 5 5 SHEET 1 AA1 9 MET A 28 GLN A 30 0 SHEET 2 AA1 9 ALA A 60 ILE A 63 1 O TRP A 62 N MET A 29 SHEET 3 AA1 9 ASN A 117 VAL A 122 1 O TYR A 119 N ILE A 61 SHEET 4 AA1 9 GLY A 248 LEU A 251 1 O ARG A 250 N VAL A 122 SHEET 5 AA1 9 PHE A 278 GLY A 281 1 O VAL A 280 N LEU A 251 SHEET 6 AA1 9 SER A 303 PHE A 305 1 O SER A 303 N GLY A 281 SHEET 7 AA1 9 ALA A 341 THR A 343 1 O VAL A 342 N LEU A 304 SHEET 8 AA1 9 TYR A 379 PHE A 383 1 O ASN A 381 N THR A 343 SHEET 9 AA1 9 MET A 28 GLN A 30 1 N MET A 28 O VAL A 382 SHEET 1 AA2 6 HIS A 126 LYS A 127 0 SHEET 2 AA2 6 SER A 220 ILE A 222 -1 O SER A 220 N LYS A 127 SHEET 3 AA2 6 PHE A 181 ASP A 187 -1 N GLY A 183 O ASN A 221 SHEET 4 AA2 6 GLU A 192 PHE A 198 -1 O GLU A 192 N ASP A 187 SHEET 5 AA2 6 PHE A 132 ASN A 142 -1 N VAL A 139 O ARG A 197 SHEET 6 AA2 6 ASN A 145 ASP A 149 -1 O GLN A 148 N ASN A 142 SHEET 1 AA3 6 HIS A 126 LYS A 127 0 SHEET 2 AA3 6 SER A 220 ILE A 222 -1 O SER A 220 N LYS A 127 SHEET 3 AA3 6 PHE A 181 ASP A 187 -1 N GLY A 183 O ASN A 221 SHEET 4 AA3 6 GLU A 192 PHE A 198 -1 O GLU A 192 N ASP A 187 SHEET 5 AA3 6 PHE A 132 ASN A 142 -1 N VAL A 139 O ARG A 197 SHEET 6 AA3 6 TYR A 154 GLY A 161 -1 O ILE A 156 N VAL A 136 SHEET 1 AA4 6 GLN A 417 TYR A 420 0 SHEET 2 AA4 6 VAL A 426 ARG A 431 -1 O GLY A 428 N TYR A 420 SHEET 3 AA4 6 LEU A 442 SER A 447 -1 O THR A 444 N TRP A 429 SHEET 4 AA4 6 SER A 494 VAL A 499 -1 O TYR A 498 N ALA A 443 SHEET 5 AA4 6 THR A 466 ASP A 469 -1 N THR A 468 O VAL A 499 SHEET 6 AA4 6 SER A 477 THR A 479 -1 O VAL A 478 N TRP A 467 SHEET 1 AA5 2 GLY A 452 TYR A 457 0 SHEET 2 AA5 2 TRP A 485 THR A 490 -1 O PHE A 488 N LYS A 454 LINK OD2 ASP A 252 C1' PBW A 601 1555 1555 1.44 LINK O4' PBW A 601 C1 GLC B 1 1555 1555 1.39 LINK CAD OC9 A 602 O4 GLC B 1 1555 1555 1.43 LINK O6 GLC B 1 C1 GLC B 2 1555 1555 1.40 LINK OD1 ASN A 125 NA NA A 605 1555 1555 2.33 LINK O ASP A 215 NA NA A 605 1555 1555 2.19 LINK OD1 ASP A 215 NA NA A 605 1555 1555 2.34 LINK OD1 ASN A 221 NA NA A 605 1555 1555 2.53 LINK O HIS A 256 NA NA A 605 1555 1555 2.38 LINK OD1 ASN A 310 NA NA A 604 1555 1555 2.38 LINK O GLY A 321 NA NA A 606 1555 1555 2.23 LINK O TYR A 323 NA NA A 606 1555 1555 2.36 LINK O VAL A 345 NA NA A 604 1555 1555 2.33 LINK OD1 ASP A 346 NA NA A 604 1555 1555 2.30 LINK O SER A 358 NA NA A 604 1555 1555 2.25 LINK O TRP A 424 NA NA A 606 1555 1555 2.57 LINK OD1 ASP A 425 NA NA A 606 1555 1555 2.41 LINK OD1 ASN A 448 NA NA A 606 1555 1555 2.72 LINK NA NA A 605 O HOH A 844 1555 1555 2.29 LINK NA NA A 606 O HOH A 859 1555 1555 2.24 CISPEP 1 TRP A 205 ARG A 206 0 -2.89 CRYST1 132.486 132.486 132.486 90.00 90.00 90.00 P 2 3 12 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 0.007548 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007548 0.00000