10 20 30 40 50 60 70 80 2HOR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE 16-JUL-06 2HOR
TITLE CRYSTAL STRUCTURE OF ALLIINASE FROM GARLIC- APO FORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALLIIN LYASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ALLIINE LYASE 1; COMPND 5 SYNONYM: ALLIINASE 1, CYSTEINE SULPHOXIDE LYASE 1; COMPND 6 EC: 4.4.1.4
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALLIUM SATIVUM; SOURCE 3 ORGANISM_COMMON: GARLIC; SOURCE 4 ORGANISM_TAXID: 4682
KEYWDS ALLIINASE; GARLIC; ALLIUM SATIVUM; GLYCOSYLATION; PLANT ENZYME; KEYWDS 2 PYRIDOXAL-5'-PHOSPHATE; AMINOACRYLATE; APO FORM;, LYASE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.J.W SHIMON,A.RABINKOV,M.WILCHECK,D.MIRELMAN,F.FROLOW
REVDAT 5 16-APR-14 2HOR 1 REMARK REVDAT 4 13-JUL-11 2HOR 1 VERSN REVDAT 3 24-FEB-09 2HOR 1 VERSN REVDAT 2 13-FEB-07 2HOR 1 JRNL REVDAT 1 06-FEB-07 2HOR 0
JRNL AUTH L.J.SHIMON,A.RABINKOV,I.SHIN,T.MIRON,D.MIRELMAN,M.WILCHEK, JRNL AUTH 2 F.FROLOW JRNL TITL TWO STRUCTURES OF ALLIINASE FROM ALLIIUM SATIVUM L.: APO JRNL TITL 2 FORM AND TERNARY COMPLEX WITH AMINOACRYLATE REACTION JRNL TITL 3 INTERMEDIATE COVALENTLY BOUND TO THE PLP COFACTOR. JRNL REF J.MOL.BIOL. V. 366 611 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17174334 JRNL DOI 10.1016/J.JMB.2006.11.041
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL ALLIIN LYASE (ALLIINASE FROM GARLIC (ALLIUM SATIVUM) REMARK 1 TITL 2 CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 58 1335 2002 REMARK 1 REFN ISSN 0907-4449
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 72527 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) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3663 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5021 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 254 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3427 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.65000 REMARK 3 B22 (A**2) : 0.65000 REMARK 3 B33 (A**2) : -1.30000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.677 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.966 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3743 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2550 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5097 ; 1.345 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6194 ; 0.884 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 455 ; 6.415 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;29.401 ;24.318 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 636 ;12.236 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;16.613 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 550 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4081 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 757 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 732 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2663 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1843 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1832 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 340 ; 0.135 ; 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): 22 ; 0.150 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 119 ; 0.238 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.125 ; 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): 2833 ; 0.801 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 880 ; 0.164 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3535 ; 0.938 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1865 ; 1.911 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1548 ; 2.520 ; 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 : 1.40 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 2HOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB038587.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9737 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72527 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.08900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 29.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : 0.52000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HAMPTON CRYSTAL SCREEN CONDITION REMARK 280 NUMBER 39, 0.1M HEPES PH 7.5, 2% V/V PEG 400 AND 2.0M AMMONIUM REMARK 280 SULFATE. THE CRYSTALS TOOK BETWEEN 4 TO 6 MONTHS TO APPEAR AND REMARK 280 GREW TO A MAXIMUM SIZE OF 0.1 X 0.1 X 0.1MM3, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 -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 82.00850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.55900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.55900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.00425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.55900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.55900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 123.01275 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.55900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.55900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.00425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.55900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.55900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 123.01275 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 82.00850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 16890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -197.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 -1.000000 0.000000 81.11800 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 81.11800 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 82.00850
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 A1162 LIES ON A SPECIAL POSITION. REMARK 375 N NO3 A 707 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 ARG A 426 REMARK 465 LYS A 427
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 55 CA CB CG CD OE1 NE2
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 GLN A 55 N GLN A 55 CA -0.271 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 GLN A 55 CA - C - O ANGL. DEV. = -15.3 DEGREES REMARK 500 GLN A 55 CA - C - N ANGL. DEV. = 14.9 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 THR A 3 -93.16 -121.10 REMARK 500 SER A 21 -155.56 52.98 REMARK 500 ARG A 89 65.31 31.72 REMARK 500 SER A 98 41.84 -153.73 REMARK 500 SER A 360 60.63 -156.62 REMARK 500 ARG A 384 38.67 70.96 REMARK 500 LYS A 406 -156.40 -89.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLN A 55 21.2 L L OUTSIDE RANGE 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 A1203 DISTANCE = 5.03 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 BMA A 504
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FUC A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BMA A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAG A 555 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 707
REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS A VARIATION IN A SEQUENCE ASSIGNEMENT IN THE REMARK 999 LITERATURE,ONE CONTAINS AN ASP IN POSITION 176 AND ONE REMARK 999 CONTAINS ASN. THE AUTHORS HAVE BUILT AND REFINED THE REMARK 999 STRUCTURE WITH AN ASP PRESENT IN THIS POSITION IN ACCORD REMARK 999 WITH THE RELATED STRUCTURE 1LK9.
DBREF 2HOR A 1 427 UNP Q01594 ALLN1_ALLSA 39 465
SEQADV 2HOR ASP A 176 UNP Q01594 ASN 214 SEE REMARK 999
SEQRES 1 A 427 LYS MET THR TRP THR MET LYS ALA ALA GLU GLU ALA GLU SEQRES 2 A 427 ALA VAL ALA ASN ILE ASN CYS SER GLU HIS GLY ARG ALA SEQRES 3 A 427 PHE LEU ASP GLY ILE ILE SER GLU GLY SER PRO LYS CYS SEQRES 4 A 427 GLU CYS ASN THR CYS TYR THR GLY PRO ASP CYS SER GLU SEQRES 5 A 427 LYS ILE GLN GLY CYS SER ALA ASP VAL ALA SER GLY ASP SEQRES 6 A 427 GLY LEU PHE LEU GLU GLU TYR TRP LYS GLN HIS LYS GLU SEQRES 7 A 427 ALA SER ALA VAL LEU VAL SER PRO TRP HIS ARG MET SER SEQRES 8 A 427 TYR PHE PHE ASN PRO VAL SER ASN PHE ILE SER PHE GLU SEQRES 9 A 427 LEU GLU LYS THR ILE LYS GLU LEU HIS GLU VAL VAL GLY SEQRES 10 A 427 ASN ALA ALA ALA LYS ASP ARG TYR ILE VAL PHE GLY VAL SEQRES 11 A 427 GLY VAL THR GLN LEU ILE HIS GLY LEU VAL ILE SER LEU SEQRES 12 A 427 SER PRO ASN MET THR ALA THR PRO ASP ALA PRO GLU SER SEQRES 13 A 427 LYS VAL VAL ALA HIS ALA PRO PHE TYR PRO VAL PHE ARG SEQRES 14 A 427 GLU GLN THR LYS TYR PHE ASP LYS LYS GLY TYR VAL TRP SEQRES 15 A 427 ALA GLY ASN ALA ALA ASN TYR VAL ASN VAL SER ASN PRO SEQRES 16 A 427 GLU GLN TYR ILE GLU MET VAL THR SER PRO ASN ASN PRO SEQRES 17 A 427 GLU GLY LEU LEU ARG HIS ALA VAL ILE LYS GLY CYS LYS SEQRES 18 A 427 SER ILE TYR ASP MET VAL TYR TYR TRP PRO HIS TYR THR SEQRES 19 A 427 PRO ILE LYS TYR LYS ALA ASP GLU ASP ILE LEU LEU PHE SEQRES 20 A 427 THR MET SER LYS PHE THR GLY HIS SER GLY SER ARG PHE SEQRES 21 A 427 GLY TRP ALA LEU ILE LYS ASP GLU SER VAL TYR ASN ASN SEQRES 22 A 427 LEU LEU ASN TYR MET THR LYS ASN THR GLU GLY THR PRO SEQRES 23 A 427 ARG GLU THR GLN LEU ARG SER LEU LYS VAL LEU LYS GLU SEQRES 24 A 427 VAL VAL ALA MET VAL LYS THR GLN LYS GLY THR MET ARG SEQRES 25 A 427 ASP LEU ASN THR PHE GLY PHE LYS LYS LEU ARG GLU ARG SEQRES 26 A 427 TRP VAL ASN ILE THR ALA LEU LEU ASP GLN SER ASP ARG SEQRES 27 A 427 PHE SER TYR GLN GLU LEU PRO GLN SER GLU TYR CYS ASN SEQRES 28 A 427 TYR PHE ARG ARG MET ARG PRO PRO SER PRO SER TYR ALA SEQRES 29 A 427 TRP VAL LYS CYS GLU TRP GLU GLU ASP LYS ASP CYS TYR SEQRES 30 A 427 GLN THR PHE GLN ASN GLY ARG ILE ASN THR GLN ASN GLY SEQRES 31 A 427 VAL GLY PHE GLU ALA SER SER ARG TYR VAL ARG LEU SER SEQRES 32 A 427 LEU ILE LYS THR GLN ASP ASP PHE ASP GLN LEU MET TYR SEQRES 33 A 427 TYR LEU LYS ASP MET VAL LYS ALA LYS ARG LYS
MODRES 2HOR ASN A 328 ASN GLYCOSYLATION SITE MODRES 2HOR ASN A 146 ASN GLYCOSYLATION SITE
HET NAG A 500 14 HET FUC A 501 10 HET NAG A 503 14 HET BMA A 504 10 HET MAN A 505 11 HET MAN A 506 12 HET NAG A 555 14 HET SO4 A 600 5 HET SO4 A 601 5 HET ACT A 602 4 HET SO4 A 701 5 HET SO4 A 702 5 HET SO4 A 703 5 HET CL A 705 1 HET CL A 706 1 HET NO3 A 707 4
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM FUC ALPHA-L-FUCOSE HETNAM BMA BETA-D-MANNOSE HETNAM MAN ALPHA-D-MANNOSE HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM CL CHLORIDE ION HETNAM NO3 NITRATE ION
FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 2 FUC C6 H12 O5 FORMUL 2 BMA C6 H12 O6 FORMUL 2 MAN 2(C6 H12 O6) FORMUL 4 SO4 5(O4 S 2-) FORMUL 6 ACT C2 H3 O2 1- FORMUL 10 CL 2(CL 1-) FORMUL 12 NO3 N O3 1- FORMUL 13 HOH *496(H2 O)
HELIX 1 1 THR A 5 ASN A 17 1 13 HELIX 2 2 GLY A 66 PHE A 68 5 3 HELIX 3 3 LEU A 69 LYS A 74 1 6 HELIX 4 4 HIS A 76 ALA A 81 1 6 HELIX 5 5 SER A 102 GLY A 117 1 16 HELIX 6 6 VAL A 130 SER A 144 1 15 HELIX 7 7 PRO A 166 PHE A 175 1 10 HELIX 8 8 ALA A 187 VAL A 190 5 4 HELIX 9 9 ASN A 194 GLU A 196 5 3 HELIX 10 10 MET A 249 THR A 253 1 5 HELIX 11 11 HIS A 255 ARG A 259 5 5 HELIX 12 12 ASP A 267 THR A 282 1 16 HELIX 13 13 PRO A 286 LYS A 308 1 23 HELIX 14 14 ASP A 313 ASP A 334 1 22 HELIX 15 15 TRP A 370 LYS A 374 5 5 HELIX 16 16 ASP A 375 GLY A 383 1 9 HELIX 17 17 VAL A 391 GLU A 394 5 4 HELIX 18 18 THR A 407 LYS A 423 1 17
SHEET 1 A 2 GLY A 24 ARG A 25 0 SHEET 2 A 2 GLU A 40 CYS A 41 -1 O GLU A 40 N ARG A 25 SHEET 1 B 2 ILE A 32 SER A 33 0 SHEET 2 B 2 SER A 36 PRO A 37 -1 O SER A 36 N SER A 33 SHEET 1 C 2 TYR A 45 THR A 46 0 SHEET 2 C 2 GLU A 52 LYS A 53 -1 O GLU A 52 N THR A 46 SHEET 1 D 2 ALA A 59 ASP A 60 0 SHEET 2 D 2 ILE A 385 ASN A 386 1 O ASN A 386 N ALA A 59 SHEET 1 E 7 TYR A 125 GLY A 129 0 SHEET 2 E 7 GLY A 261 ILE A 265 -1 O ILE A 265 N TYR A 125 SHEET 3 E 7 ILE A 244 THR A 248 -1 N LEU A 245 O LEU A 264 SHEET 4 E 7 LYS A 221 ASP A 225 1 N TYR A 224 O LEU A 246 SHEET 5 E 7 TYR A 198 THR A 203 1 N VAL A 202 O ASP A 225 SHEET 6 E 7 SER A 156 ALA A 160 1 N VAL A 159 O MET A 201 SHEET 7 E 7 TYR A 180 ASN A 185 1 O ALA A 183 N VAL A 158 SHEET 1 F 4 PHE A 339 SER A 340 0 SHEET 2 F 4 TYR A 363 CYS A 368 -1 O LYS A 367 N SER A 340 SHEET 3 F 4 TYR A 399 SER A 403 -1 O LEU A 402 N ALA A 364 SHEET 4 F 4 GLN A 388 ASN A 389 -1 N GLN A 388 O ARG A 401 SHEET 1 G 2 GLU A 348 CYS A 350 0 SHEET 2 G 2 ARG A 355 ARG A 357 -1 O ARG A 355 N CYS A 350
SSBOND 1 CYS A 20 CYS A 39 1555 1555 2.03 SSBOND 2 CYS A 41 CYS A 50 1555 1555 2.05 SSBOND 3 CYS A 44 CYS A 57 1555 1555 2.05 SSBOND 4 CYS A 368 CYS A 376 1555 1555 2.05
LINK ND2 ASN A 328 C1 NAG A 555 1555 1555 1.45 LINK ND2 ASN A 146 C1 NAG A 500 1555 1555 1.42 LINK O4 NAG A 500 C1 NAG A 503 1555 1555 1.44 LINK O4 NAG A 503 C1 BMA A 504 1555 1555 1.44 LINK O6 BMA A 504 C1 MAN A 505 1555 1555 1.44 LINK C3 BMA A 504 O2 MAN A 506 1555 1555 1.34 LINK O3 NAG A 500 C1 FUC A 501 1555 1555 1.46
CISPEP 1 ASN A 95 PRO A 96 0 3.05 CISPEP 2 ALA A 162 PRO A 163 0 1.31 CISPEP 3 SER A 204 PRO A 205 0 -7.83 CISPEP 4 ASN A 207 PRO A 208 0 16.67
SITE 1 AC1 10 ASN A 146 ALA A 149 TYR A 174 FUC A 501 SITE 2 AC1 10 NAG A 503 SO4 A 701 HOH A 849 HOH A 875 SITE 3 AC1 10 HOH A1124 HOH A1131 SITE 1 AC2 8 GLU A 170 ASN A 276 LYS A 280 NAG A 500 SITE 2 AC2 8 NAG A 503 HOH A 849 HOH A 875 HOH A1137 SITE 1 AC3 9 THR A 148 LYS A 173 NAG A 500 FUC A 501 SITE 2 AC3 9 BMA A 504 SO4 A 701 HOH A 849 HOH A 991 SITE 3 AC3 9 HOH A1116 SITE 1 AC4 7 NAG A 503 MAN A 505 MAN A 506 HOH A1174 SITE 2 AC4 7 HOH A1177 HOH A1178 HOH A1201 SITE 1 AC5 3 VAL A 391 BMA A 504 HOH A 995 SITE 1 AC6 4 GLU A 114 BMA A 504 HOH A 876 HOH A1005 SITE 1 AC7 6 ASN A 328 GLN A 408 PHE A 411 HOH A 942 SITE 2 AC7 6 HOH A1018 HOH A1098 SITE 1 AC8 11 GLY A 64 TYR A 165 ASN A 207 LYS A 251 SITE 2 AC8 11 GLN A 388 ARG A 401 HOH A 777 HOH A 789 SITE 3 AC8 11 HOH A 944 HOH A1095 HOH A1185 SITE 1 AC9 10 TYR A 92 GLY A 131 VAL A 132 THR A 133 SITE 2 AC9 10 THR A 248 SER A 250 ARG A 259 HOH A 766 SITE 3 AC9 10 HOH A1053 HOH A1096 SITE 1 BC1 6 TYR A 165 ASP A 225 VAL A 227 HOH A 766 SITE 2 BC1 6 HOH A1095 HOH A1096 SITE 1 BC2 3 NAG A 500 NAG A 503 HOH A1201 SITE 1 BC3 7 GLU A 22 ASN A 42 THR A 407 GLN A 408 SITE 2 BC3 7 ASP A 409 HOH A 971 HOH A1115 SITE 1 BC4 6 LYS A 74 GLN A 75 HIS A 76 LYS A 77 SITE 2 BC4 6 GLU A 78 HOH A 735 SITE 1 BC5 4 PHE A 93 PHE A 94 SER A 98 PHE A 100 SITE 1 BC6 2 GLU A 114 HOH A1192 SITE 1 BC7 4 HIS A 137 PHE A 175 LYS A 177 HOH A1162
CRYST1 81.118 81.118 164.017 90.00 90.00 90.00 P 41 21 2 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 0.012328 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012328 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006097 0.00000