HEADER HYDROLASE 06-JAN-22 7WJC TITLE CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS SUBSP. CREMORIS GH31 ALPHA-1, TITLE 2 3-GLUCOSIDASE MUTANT D394A IN COMPLEX WITH NIGEROSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-XYLOSIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. CREMORIS MG1363; SOURCE 3 ORGANISM_TAXID: 416870; SOURCE 4 STRAIN: MG1363; SOURCE 5 GENE: LLMG_1836; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS NIGEROSE, GLUCOSE, GLYCOSIDE HYDROLASE, GH31, CARBOHYDRATE, TIM- KEYWDS 2 BARREL, HEXAMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.IKEGAYA,T.MIYAZAKI REVDAT 3 29-NOV-23 7WJC 1 REMARK REVDAT 2 11-MAY-22 7WJC 1 JRNL REVDAT 1 30-MAR-22 7WJC 0 JRNL AUTH M.IKEGAYA,T.MORIYA,N.ADACHI,M.KAWASAKI,E.Y.PARK,T.MIYAZAKI JRNL TITL STRUCTURAL BASIS OF THE STRICT SPECIFICITY OF A BACTERIAL JRNL TITL 2 GH31 ALPHA-1,3-GLUCOSIDASE FOR NIGEROOLIGOSACCHARIDES. JRNL REF J.BIOL.CHEM. V. 298 01827 2022 JRNL REFN ESSN 1083-351X JRNL PMID 35293315 JRNL DOI 10.1016/J.JBC.2022.101827 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 120083 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 451 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5988 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 552 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52500 REMARK 3 B22 (A**2) : 0.52500 REMARK 3 B33 (A**2) : -1.70200 REMARK 3 B12 (A**2) : 0.26200 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.058 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6241 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5687 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8439 ; 1.613 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13136 ; 1.444 ; 1.583 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 735 ; 7.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;35.028 ;23.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1054 ;12.505 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;12.608 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 777 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7064 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1506 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1163 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 82 ; 0.191 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3000 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 449 ; 0.124 ; 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): 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): 2928 ; 2.473 ; 3.196 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2927 ; 2.468 ; 3.196 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3661 ; 3.035 ; 4.783 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3662 ; 3.036 ; 4.783 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3313 ; 3.533 ; 3.498 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3314 ; 3.533 ; 3.498 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4776 ; 5.182 ; 5.097 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4777 ; 5.181 ; 5.097 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 PLUS 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7WJC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1300025923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.00 REMARK 200 R MERGE FOR SHELL (I) : 1.19100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 7WJA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13% PEG 3350, 400 MM AMMONIUM CITRATE REMARK 280 BUFFER (PH 7.0), 10 MM NIGEROSE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 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 88.61750 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 88.61750 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 88.61750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 88.61750 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 88.61750 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 88.61750 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 42170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 150810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 152.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 151.37000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 75.68500 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 131.09027 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 75.68500 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 131.09027 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 88.61750 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 151.37000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 88.61750 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 88.61750 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 6 REMARK 465 SER A 7 REMARK 465 LYS A 8 REMARK 465 TYR A 9 REMARK 465 MET A 10 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 580 CD GLU A 580 OE1 0.125 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 ASP A 18 -129.11 49.82 REMARK 500 LYS A 93 53.95 -92.71 REMARK 500 TYR A 99 36.04 -151.16 REMARK 500 LYS A 114 174.04 72.72 REMARK 500 VAL A 237 -79.89 -125.80 REMARK 500 ASP A 312 82.18 -156.04 REMARK 500 VAL A 326 -61.81 -107.21 REMARK 500 ASP A 341 77.51 -119.15 REMARK 500 GLN A 429 -146.73 50.75 REMARK 500 ASP A 433 105.62 -165.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 7WJC A 1 739 UNP A2RM80 A2RM80_LACLM 1 739 SEQADV 7WJC MET A -19 UNP A2RM80 INITIATING METHIONINE SEQADV 7WJC GLY A -18 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC SER A -17 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC SER A -16 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -15 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -14 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -13 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -12 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -11 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A -10 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC SER A -9 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC SER A -8 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC GLY A -7 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC LEU A -6 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC VAL A -5 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC PRO A -4 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC ARG A -3 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC GLY A -2 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC SER A -1 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC HIS A 0 UNP A2RM80 EXPRESSION TAG SEQADV 7WJC ALA A 394 UNP A2RM80 ASP 394 ENGINEERED MUTATION SEQRES 1 A 759 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 759 LEU VAL PRO ARG GLY SER HIS MET VAL SER GLU LEU GLU SEQRES 3 A 759 SER LYS TYR MET ASN ASN ASN ILE ILE LYS PHE ASP LYS SEQRES 4 A 759 ALA ARG PHE THR VAL LEU THR GLU HIS LEU ILE ARG ILE SEQRES 5 A 759 GLU TYR SER GLU THR GLY GLU PHE GLU GLU ARG MET THR SEQRES 6 A 759 GLN MET VAL GLN ASN ARG GLU PHE SER GLU VAL ASN PHE SEQRES 7 A 759 ASP ILE ILE GLU LYS GLU GLU THR ILE GLU ILE ILE THR SEQRES 8 A 759 SER THR VAL HIS LEU TYR TYR ASN GLY GLY GLU PHE THR SEQRES 9 A 759 ASN ALA SER LEU PHE ALA ASP VAL LYS PHE ASN PHE SER SEQRES 10 A 759 VAL TYR SER ASN ARG TRP TYR PHE GLY GLU LYS SER ASP SEQRES 11 A 759 GLY ASN LEU LYS GLY THR THR ARG THR LEU ASP MET ILE SEQRES 12 A 759 ASP GLY GLU CYS PRO LEU GLU ASP GLY ILE MET SER LYS SEQRES 13 A 759 ASN GLY PHE ALA VAL LEU ALA ASP LYS GLY LYS VAL LEU SEQRES 14 A 759 THR GLU VAL GLY ASP ILE ALA GLY ASN SER VAL SER THR SEQRES 15 A 759 ILE ASP LEU TYR LEU PHE ALA TYR GLY ARG ASP TYR ARG SEQRES 16 A 759 GLN ALA LEU LYS ASP PHE TYR GLN LEU THR GLY ASN THR SEQRES 17 A 759 PRO LYS LEU PRO ARG PHE ALA LEU GLY ASN TRP TRP SER SEQRES 18 A 759 ARG TYR TYR ASP TYR SER ASP LYS SER TYR LEU ALA LEU SEQRES 19 A 759 MET ASP LYS PHE THR ASP LYS LYS VAL PRO LEU SER VAL SEQRES 20 A 759 SER VAL ILE ASP MET ASP TRP HIS LYS VAL SER GLU VAL SEQRES 21 A 759 PRO SER ARG PHE GLY SER GLY TRP THR GLY TYR SER TRP SEQRES 22 A 759 ASN LYS LYS LEU PHE PRO ASN PRO GLU ASN PHE ILE ASP SEQRES 23 A 759 GLU LEU HIS GLN ARG LYS LEU LYS VAL THR LEU ASN ASP SEQRES 24 A 759 HIS PRO ALA ASP GLY ILE ARG ALA PHE GLU ASP PRO TYR SEQRES 25 A 759 PRO GLN VAL ALA GLN THR LEU ASP LEU ASN THR GLU LEU SEQRES 26 A 759 GLU GLU ALA ALA LYS PHE ASP PHE ASP ASN LEU LYS PHE SEQRES 27 A 759 ARG LYS ALA TYR PHE GLU GLU VAL HIS GLY PRO LEU GLU SEQRES 28 A 759 LYS GLU GLY VAL ASP PHE TRP TRP ILE ASP TRP GLN GLN SEQRES 29 A 759 GLY ALA ILE SER LYS SER GLY VAL ASP PRO LEU TRP LEU SEQRES 30 A 759 LEU ASN HIS TYR GLN TYR GLN ASN ALA GLN LYS LYS HIS SEQRES 31 A 759 LYS ASN ASN ILE ILE LEU SER ARG TYR ALA GLY PRO GLY SEQRES 32 A 759 SER HIS ARG TYR PRO LEU GLY PHE SER GLY ALA SER VAL SEQRES 33 A 759 ILE SER TRP ALA SER LEU ASP PHE GLN PRO TYR PHE THR SEQRES 34 A 759 SER THR ALA SER ASN ILE GLY TYR THR TRP TRP SER HIS SEQRES 35 A 759 ASP ILE GLY GLY HIS MET GLN GLY TYR LYS ASP ALA GLU SEQRES 36 A 759 LEU SER LEU ARG TRP LEU GLN PHE GLY VAL PHE SER PRO SEQRES 37 A 759 ILE ASN ARG LEU HIS SER SER LYS SER GLU PHE THR SER SEQRES 38 A 759 LYS GLU PRO TRP HIS PHE ASP ALA VAL ILE GLU GLN SER SEQRES 39 A 759 MET ILE ASP PHE LEU GLN LEU ARG HIS GLN LEU ILE PRO SEQRES 40 A 759 TYR LEU TYR SER ALA ASN LEU ILE THR ALA SER GLU GLY SEQRES 41 A 759 ARG ALA LEU VAL GLU PRO LEU TYR TYR GLU TYR PRO MET SEQRES 42 A 759 GLU GLU GLU ALA TYR GLN HIS ARG ASN GLN TYR LEU PHE SEQRES 43 A 759 GLY GLU GLN LEU MET VAL ALA PRO ILE THR GLU LYS MET SEQRES 44 A 759 ASN SER LEU LEU GLN MET GLY SER VAL GLU VAL TRP PHE SEQRES 45 A 759 PRO GLU GLY THR TRP TYR ASP PHE PHE SER GLY GLN PRO SEQRES 46 A 759 TYR ASP GLY LYS VAL SER LEU LYS VAL TYR ARG GLU ILE SEQRES 47 A 759 THR GLU MET PRO VAL PHE ALA LYS ALA GLY ALA ILE ILE SEQRES 48 A 759 PRO LEU ASP LYS ASN PRO LEU LYS LYS GLU GLU ILE PRO SEQRES 49 A 759 SER GLU ILE ILE TRP LYS ILE PHE PRO GLY ALA ASP GLY SEQRES 50 A 759 GLU TYR LEU LEU LEU GLU GLU ASP ASN GLU THR LYS ALA SEQRES 51 A 759 GLU PHE VAL ASN GLY ILE PHE THR VAL THR SER LYS LYS SEQRES 52 A 759 GLU SER SER ARG LYS HIS THR ILE ILE TYR GLY GLU HIS SEQRES 53 A 759 GLU ILE VAL SER ALA LYS ARG GLY GLU PHE SER ILE ASP SEQRES 54 A 759 LEU ASN GLY LYS GLU GLU ASN PHE ASP TRP ASN PHE SER SEQRES 55 A 759 THR ALA LEU PHE ARG ARG LEU ASP ILE ALA GLU ILE SER SEQRES 56 A 759 TYR GLU GLN LYS ASP GLU ILE LEU GLN GLN LEU SER LEU SEQRES 57 A 759 ILE GLU GLU HIS GLU LYS GLN VAL ALA PHE ILE LYS THR SEQRES 58 A 759 ASN GLU ASN GLN GLU LEU GLN ASN SER LEU PHE GLU LEU SEQRES 59 A 759 LEU TYR SER GLY LYS HET GLC B 1 12 HET GLC B 2 11 HET EDO A 801 4 HET EDO A 802 4 HET EDO A 803 4 HET EDO A 804 4 HET EDO A 805 4 HET EDO A 806 4 HET EDO A 807 4 HET EDO A 808 4 HET EDO A 809 4 HET EDO A 810 4 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GLC 2(C6 H12 O6) FORMUL 3 EDO 10(C2 H6 O2) FORMUL 13 HOH *552(H2 O) HELIX 1 AA1 ASP A 173 GLY A 186 1 14 HELIX 2 AA2 PRO A 192 LEU A 196 5 5 HELIX 3 AA3 SER A 207 LYS A 221 1 15 HELIX 4 AA4 ASP A 231 HIS A 235 5 5 HELIX 5 AA5 PRO A 241 GLY A 245 5 5 HELIX 6 AA6 ASN A 260 ARG A 271 1 12 HELIX 7 AA7 HIS A 280 GLY A 284 5 5 HELIX 8 AA8 PRO A 291 LEU A 299 1 9 HELIX 9 AA9 ASN A 315 VAL A 326 1 12 HELIX 10 AB1 VAL A 326 GLY A 334 1 9 HELIX 11 AB2 ASP A 353 GLN A 367 1 15 HELIX 12 AB3 GLY A 383 TYR A 387 5 5 HELIX 13 AB4 SER A 398 ALA A 412 1 15 HELIX 14 AB5 SER A 413 GLY A 416 5 4 HELIX 15 AB6 ASP A 433 PHE A 446 1 14 HELIX 16 AB7 GLU A 463 PHE A 467 5 5 HELIX 17 AB8 ASP A 468 LEU A 485 1 18 HELIX 18 AB9 LEU A 485 GLY A 500 1 16 HELIX 19 AC1 LEU A 507 TYR A 511 1 5 HELIX 20 AC2 GLU A 514 GLN A 519 5 6 HELIX 21 AC3 ASN A 680 ALA A 692 1 13 HELIX 22 AC4 SER A 695 ILE A 709 1 15 HELIX 23 AC5 GLU A 711 THR A 721 1 11 HELIX 24 AC6 ASN A 724 GLY A 738 1 15 SHEET 1 AA1 5 ILE A 14 PHE A 17 0 SHEET 2 AA1 5 ALA A 20 THR A 26 -1 O PHE A 22 N ILE A 15 SHEET 3 AA1 5 LEU A 29 TYR A 34 -1 O GLU A 33 N ARG A 21 SHEET 4 AA1 5 ILE A 163 PHE A 168 -1 O LEU A 167 N ILE A 30 SHEET 5 AA1 5 ALA A 140 ALA A 143 -1 N ALA A 140 O PHE A 168 SHEET 1 AA2 5 ASP A 59 GLU A 62 0 SHEET 2 AA2 5 ILE A 67 ILE A 70 -1 O ILE A 70 N ASP A 59 SHEET 3 AA2 5 VAL A 74 TYR A 78 -1 O LEU A 76 N ILE A 69 SHEET 4 AA2 5 LEU A 88 VAL A 92 -1 O PHE A 89 N TYR A 77 SHEET 5 AA2 5 ARG A 102 TYR A 104 -1 O TRP A 103 N ALA A 90 SHEET 1 AA3 2 VAL A 148 LEU A 149 0 SHEET 2 AA3 2 ILE A 155 GLY A 157 -1 O ALA A 156 N VAL A 148 SHEET 1 AA4 7 ILE A 375 LEU A 376 0 SHEET 2 AA4 7 PHE A 337 ILE A 340 1 N ILE A 340 O LEU A 376 SHEET 3 AA4 7 LYS A 274 ASP A 279 1 N ASP A 279 O TRP A 339 SHEET 4 AA4 7 VAL A 227 ILE A 230 1 N SER A 228 O LYS A 274 SHEET 5 AA4 7 ASN A 198 TRP A 200 1 N TRP A 200 O VAL A 229 SHEET 6 AA4 7 ASN A 450 LEU A 452 1 O LEU A 452 N TRP A 199 SHEET 7 AA4 7 ASP A 423 ILE A 424 1 N ILE A 424 O ARG A 451 SHEET 1 AA5 2 GLY A 390 PHE A 391 0 SHEET 2 AA5 2 TRP A 420 SER A 421 1 O SER A 421 N GLY A 390 SHEET 1 AA6 6 VAL A 504 PRO A 506 0 SHEET 2 AA6 6 TYR A 524 PHE A 526 -1 O LEU A 525 N GLU A 505 SHEET 3 AA6 6 LEU A 530 VAL A 532 -1 O VAL A 532 N TYR A 524 SHEET 4 AA6 6 VAL A 583 LYS A 586 -1 O PHE A 584 N MET A 531 SHEET 5 AA6 6 THR A 556 ASP A 559 -1 N TYR A 558 O ALA A 585 SHEET 6 AA6 6 PRO A 565 ASP A 567 -1 O TYR A 566 N TRP A 557 SHEET 1 AA7 2 GLY A 546 PHE A 552 0 SHEET 2 AA7 2 VAL A 570 ARG A 576 -1 O VAL A 570 N PHE A 552 SHEET 1 AA8 4 ILE A 590 ASP A 594 0 SHEET 2 AA8 4 GLU A 606 ILE A 611 -1 O ILE A 608 N LEU A 593 SHEET 3 AA8 4 LYS A 648 TYR A 653 1 O THR A 650 N ILE A 607 SHEET 4 AA8 4 HIS A 656 ARG A 663 -1 O LYS A 662 N HIS A 649 SHEET 1 AA9 4 GLY A 617 GLU A 623 0 SHEET 2 AA9 4 ASN A 626 VAL A 633 -1 O THR A 628 N LEU A 621 SHEET 3 AA9 4 ILE A 636 SER A 641 -1 O THR A 638 N GLU A 631 SHEET 4 AA9 4 PHE A 666 ASP A 669 -1 O PHE A 666 N VAL A 639 LINK O3 GLC B 1 C1 GLC B 2 1555 1555 1.47 CISPEP 1 PRO A 388 LEU A 389 0 10.12 CISPEP 2 GLY A 568 LYS A 569 0 -7.63 CRYST1 151.370 151.370 177.235 90.00 90.00 120.00 P 63 2 2 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 0.006606 0.003814 0.000000 0.00000 SCALE2 0.000000 0.007628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005642 0.00000