HEADER HYDROLASE 06-FEB-07 2OSX TITLE ENDO-GLYCOCERAMIDASE II FROM RHODOCOCCUS SP.: GANGLIOSIDE GM3 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOGLYCOCERAMIDASE II; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.123; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOCOCCUS SP.; SOURCE 3 ORGANISM_TAXID: 1831; SOURCE 4 STRAIN: M-777; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(TUNER); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A(+) KEYWDS (ALPHA/BETA)8 (TIM) BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.E.C.CAINES,N.C.J.STRYNADKA REVDAT 8 21-FEB-24 2OSX 1 REMARK REVDAT 7 20-OCT-21 2OSX 1 REMARK SEQADV HETSYN REVDAT 6 29-JUL-20 2OSX 1 COMPND REMARK SEQADV HETNAM REVDAT 6 2 1 HETSYN LINK SITE ATOM REVDAT 5 13-JUL-11 2OSX 1 VERSN REVDAT 4 21-JUL-09 2OSX 1 HETATM REVDAT 3 24-FEB-09 2OSX 1 VERSN REVDAT 2 29-MAY-07 2OSX 1 JRNL REVDAT 1 27-FEB-07 2OSX 0 JRNL AUTH M.E.CAINES,M.D.VAUGHAN,C.A.TARLING,S.M.HANCOCK,R.A.WARREN, JRNL AUTH 2 S.G.WITHERS,N.C.STRYNADKA JRNL TITL STRUCTURAL AND MECHANISTIC ANALYSES OF ENDO-GLYCOCERAMIDASE JRNL TITL 2 II, A MEMBRANE-ASSOCIATED FAMILY 5 GLYCOSIDASE IN THE APO JRNL TITL 3 AND GM3 GANGLIOSIDE-BOUND FORMS. JRNL REF J.BIOL.CHEM. V. 282 14300 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17329247 JRNL DOI 10.1074/JBC.M611455200 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 171710 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) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.139 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 8690 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) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11509 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 601 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 598 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.026 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.026 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.014 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.633 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3769 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2540 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5190 ; 1.468 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6155 ; 0.955 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 496 ; 6.178 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;31.712 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 528 ;11.374 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;12.930 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 566 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4315 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 784 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 762 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2884 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1890 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1907 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 388 ; 0.131 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.130 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 6 ; 0.348 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 24 ; 0.292 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.151 ; 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 ; 1.159 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 944 ; 0.596 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3778 ; 1.742 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1510 ; 2.206 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1392 ; 2.942 ; 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): 6703 ; 0.975 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 619 ; 6.678 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6186 ; 3.680 ; 3.000 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 : 1.40 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 2OSX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL, SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 171712 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 31.734 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : 0.05400 REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.46300 REMARK 200 R SYM FOR SHELL (I) : 0.46300 REMARK 200 FOR SHELL : 1.500 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 3350; 0.175 M NACL; 0.1 REMARK 280 M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 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 38.90050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.99200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.90050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.99200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS BELIEVED TO BE A MONOMER. 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 A1028 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1163 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 10 REMARK 465 GLY A 11 REMARK 465 SER A 12 REMARK 465 SER A 13 REMARK 465 HIS A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 SER A 20 REMARK 465 SER A 21 REMARK 465 GLY A 22 REMARK 465 LEU A 23 REMARK 465 VAL A 24 REMARK 465 PRO A 25 REMARK 465 ARG A 26 REMARK 465 GLY A 27 REMARK 465 SER A 28 REMARK 465 HIS A 29 REMARK 465 MET A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 SER A 33 REMARK 465 GLY A 34 REMARK 465 SER A 35 REMARK 465 GLY A 36 REMARK 465 SER A 37 REMARK 465 GLY A 38 REMARK 465 THR A 39 REMARK 465 ALA A 40 REMARK 465 LEU A 41 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 74 CG CD OE1 NE2 REMARK 480 GLU A 125 CG CD OE1 OE2 REMARK 480 GLU A 146 CG CD OE1 OE2 REMARK 480 ARG A 255 CG CD NE CZ NH1 NH2 REMARK 480 GLN A 296 CG CD OE1 NE2 REMARK 480 GLU A 419 CG CD OE1 OE2 REMARK 480 GLU A 432 CG CD OE1 OE2 REMARK 480 GLU A 447 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 OE1 GLN A 296 O HOH A 1025 2.04 REMARK 500 REMARK 500 REMARK: NULL 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 146 CB GLU A 146 CG 0.154 REMARK 500 GLU A 419 CB GLU A 419 CG -0.122 REMARK 500 GLU A 432 CB GLU A 432 CG -0.204 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 93 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 MET A 131 CG - SD - CE ANGL. DEV. = -12.6 DEGREES REMARK 500 GLU A 146 CA - CB - CG ANGL. DEV. = -13.6 DEGREES REMARK 500 GLU A 419 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 GLU A 432 CA - CB - CG ANGL. DEV. = 19.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 139 -58.24 74.88 REMARK 500 ILE A 156 -87.00 -109.75 REMARK 500 REMARK 500 REMARK: NULL 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 16C A 603 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 607 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 69 O REMARK 620 2 HOH A 671 O 82.8 REMARK 620 3 HOH A 703 O 169.6 94.3 REMARK 620 4 HOH A1053 O 88.4 100.6 82.3 REMARK 620 5 HOH A1166 O 98.8 152.2 88.4 107.2 REMARK 620 N 1 2 3 4 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 ALA A 162 O REMARK 620 2 THR A 165 O 95.0 REMARK 620 3 HOH A 797 O 97.8 80.1 REMARK 620 4 HOH A 797 O 111.0 108.1 32.6 REMARK 620 5 HOH A 923 O 87.9 105.3 171.8 139.5 REMARK 620 6 HOH A 979 O 86.2 169.2 89.1 61.7 85.5 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 222 O REMARK 620 2 VAL A 225 O 98.4 REMARK 620 3 HOH A 696 O 91.6 87.6 REMARK 620 4 HOH A 717 O 166.6 93.8 83.3 REMARK 620 5 HOH A 745 O 97.2 87.2 170.3 88.9 REMARK 620 6 HOH A 758 O 83.9 175.9 95.8 84.2 89.1 REMARK 620 N 1 2 3 4 5 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 ASP A 291 O REMARK 620 2 GLN A 297 OE1 91.8 REMARK 620 3 HOH A 676 O 76.5 106.1 REMARK 620 4 HOH A 847 O 85.6 82.8 160.1 REMARK 620 5 HOH A 976 O 173.5 87.5 97.4 100.8 REMARK 620 6 HOH A 988 O 82.7 169.6 81.2 88.0 99.0 REMARK 620 N 1 2 3 4 5 DBREF 2OSX A 31 490 UNP O33853 O33853_RHOSO 31 490 SEQADV 2OSX MET A 10 UNP O33853 CLONING ARTIFACT SEQADV 2OSX GLY A 11 UNP O33853 CLONING ARTIFACT SEQADV 2OSX SER A 12 UNP O33853 CLONING ARTIFACT SEQADV 2OSX SER A 13 UNP O33853 CLONING ARTIFACT SEQADV 2OSX HIS A 14 UNP O33853 EXPRESSION TAG SEQADV 2OSX HIS A 15 UNP O33853 EXPRESSION TAG SEQADV 2OSX HIS A 16 UNP O33853 EXPRESSION TAG SEQADV 2OSX HIS A 17 UNP O33853 EXPRESSION TAG SEQADV 2OSX HIS A 18 UNP O33853 EXPRESSION TAG SEQADV 2OSX HIS A 19 UNP O33853 EXPRESSION TAG SEQADV 2OSX SER A 20 UNP O33853 CLONING ARTIFACT SEQADV 2OSX SER A 21 UNP O33853 CLONING ARTIFACT SEQADV 2OSX GLY A 22 UNP O33853 CLONING ARTIFACT SEQADV 2OSX LEU A 23 UNP O33853 CLONING ARTIFACT SEQADV 2OSX VAL A 24 UNP O33853 CLONING ARTIFACT SEQADV 2OSX PRO A 25 UNP O33853 CLONING ARTIFACT SEQADV 2OSX ARG A 26 UNP O33853 CLONING ARTIFACT SEQADV 2OSX GLY A 27 UNP O33853 CLONING ARTIFACT SEQADV 2OSX SER A 28 UNP O33853 CLONING ARTIFACT SEQADV 2OSX HIS A 29 UNP O33853 CLONING ARTIFACT SEQADV 2OSX MET A 30 UNP O33853 CLONING ARTIFACT SEQADV 2OSX SER A 351 UNP O33853 GLU 351 ENGINEERED MUTATION SEQRES 1 A 481 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 481 LEU VAL PRO ARG GLY SER HIS MET SER GLY SER GLY SER SEQRES 3 A 481 GLY SER GLY THR ALA LEU THR PRO SER TYR LEU LYS ASP SEQRES 4 A 481 ASP ASP GLY ARG SER LEU ILE LEU ARG GLY PHE ASN THR SEQRES 5 A 481 ALA SER SER ALA LYS SER ALA PRO ASP GLY MET PRO GLN SEQRES 6 A 481 PHE THR GLU ALA ASP LEU ALA ARG GLU TYR ALA ASP MET SEQRES 7 A 481 GLY THR ASN PHE VAL ARG PHE LEU ILE SER TRP ARG SER SEQRES 8 A 481 VAL GLU PRO ALA PRO GLY VAL TYR ASP GLN GLN TYR LEU SEQRES 9 A 481 ASP ARG VAL GLU ASP ARG VAL GLY TRP TYR ALA GLU ARG SEQRES 10 A 481 GLY TYR LYS VAL MET LEU ASP MET HIS GLN ASP VAL TYR SEQRES 11 A 481 SER GLY ALA ILE THR PRO GLU GLY ASN SER GLY ASN GLY SEQRES 12 A 481 ALA GLY ALA ILE GLY ASN GLY ALA PRO ALA TRP ALA THR SEQRES 13 A 481 TYR MET ASP GLY LEU PRO VAL GLU PRO GLN PRO ARG TRP SEQRES 14 A 481 GLU LEU TYR TYR ILE GLN PRO GLY VAL MET ARG ALA PHE SEQRES 15 A 481 ASP ASN PHE TRP ASN THR THR GLY LYS HIS PRO GLU LEU SEQRES 16 A 481 VAL GLU HIS TYR ALA LYS ALA TRP ARG ALA VAL ALA ASP SEQRES 17 A 481 ARG PHE ALA ASP ASN ASP ALA VAL VAL ALA TYR ASP LEU SEQRES 18 A 481 MET ASN GLU PRO PHE GLY GLY SER LEU GLN GLY PRO ALA SEQRES 19 A 481 PHE GLU ALA GLY PRO LEU ALA ALA MET TYR GLN ARG THR SEQRES 20 A 481 THR ASP ALA ILE ARG GLN VAL ASP GLN ASP THR TRP VAL SEQRES 21 A 481 CYS VAL ALA PRO GLN ALA ILE GLY VAL ASN GLN GLY LEU SEQRES 22 A 481 PRO SER GLY LEU THR LYS ILE ASP ASP PRO ARG ALA GLY SEQRES 23 A 481 GLN GLN ARG ILE ALA TYR CYS PRO HIS LEU TYR PRO LEU SEQRES 24 A 481 PRO LEU ASP ILE GLY ASP GLY HIS GLU GLY LEU ALA ARG SEQRES 25 A 481 THR LEU THR ASP VAL THR ILE ASP ALA TRP ARG ALA ASN SEQRES 26 A 481 THR ALA HIS THR ALA ARG VAL LEU GLY ASP VAL PRO ILE SEQRES 27 A 481 ILE LEU GLY SER PHE GLY LEU ASP THR THR LEU PRO GLY SEQRES 28 A 481 ALA ARG ASP TYR ILE GLU ARG VAL TYR GLY THR ALA ARG SEQRES 29 A 481 GLU MET GLY ALA GLY VAL SER TYR TRP SER SER ASP PRO SEQRES 30 A 481 GLY PRO TRP GLY PRO TYR LEU PRO ASP GLY THR GLN THR SEQRES 31 A 481 LEU LEU VAL ASP THR LEU ASN LYS PRO TYR PRO ARG ALA SEQRES 32 A 481 VAL ALA GLY THR PRO THR GLU TRP SER SER THR SER ASP SEQRES 33 A 481 ARG LEU GLN LEU THR ILE GLU PRO ASP ALA ALA ILE THR SEQRES 34 A 481 ALA PRO THR GLU ILE TYR LEU PRO GLU ALA GLY PHE PRO SEQRES 35 A 481 GLY ASP VAL HIS VAL GLU GLY ALA ASP VAL VAL GLY TRP SEQRES 36 A 481 ASP ARG GLN SER ARG LEU LEU THR VAL ARG THR PRO ALA SEQRES 37 A 481 ASP SER GLY ASN VAL THR VAL THR VAL THR PRO ALA ALA HET BGC B 1 11 HET GAL B 2 11 HET SIA B 3 20 HET NA A 604 1 HET NA A 605 1 HET NA A 606 1 HET NA A 607 1 HET 16C A 603 21 HET GOL A 608 6 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID HETNAM NA SODIUM ION HETNAM 16C N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)PALMITAMIDE HETNAM GOL GLYCEROL HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID HETSYN 16C C16-CERAMIDE; N-PALMITOYL-D-ERYTHRO-SPHINGOSINE; (2S, HETSYN 2 16C 3R,4E)-2-PALMITOYLAMINOOCTADEC-4-ENE-1,3-DIOL; (2S,3R, HETSYN 3 16C 4E)-2-PALMITOYLAMINO-1,3-OCTADEC-4-ENEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 BGC C6 H12 O6 FORMUL 2 GAL C6 H12 O6 FORMUL 2 SIA C11 H19 N O9 FORMUL 3 NA 4(NA 1+) FORMUL 7 16C C34 H67 N O3 FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *598(H2 O) HELIX 1 1 ALA A 62 SER A 67 5 6 HELIX 2 2 THR A 76 GLY A 88 1 13 HELIX 3 3 SER A 97 GLU A 102 1 6 HELIX 4 4 ASP A 109 ARG A 126 1 18 HELIX 5 5 SER A 140 THR A 144 5 5 HELIX 6 6 PRO A 161 THR A 165 5 5 HELIX 7 7 ARG A 177 ILE A 183 5 7 HELIX 8 8 GLN A 184 TRP A 195 1 12 HELIX 9 9 PRO A 202 ALA A 220 1 19 HELIX 10 10 GLY A 241 ALA A 246 1 6 HELIX 11 11 GLY A 247 ARG A 261 1 15 HELIX 12 12 GLY A 277 GLY A 281 5 5 HELIX 13 13 PRO A 307 GLY A 313 1 7 HELIX 14 14 GLU A 317 LEU A 342 1 26 HELIX 15 15 GLY A 360 GLY A 376 1 17 HELIX 16 16 LEU A 400 ASN A 406 1 7 SHEET 1 A 5 SER A 53 LEU A 54 0 SHEET 2 A 5 TYR A 409 VAL A 413 -1 O VAL A 413 N SER A 53 SHEET 3 A 5 THR A 441 TYR A 444 -1 O GLU A 442 N ALA A 412 SHEET 4 A 5 LEU A 470 ARG A 474 -1 O LEU A 471 N ILE A 443 SHEET 5 A 5 ASP A 460 ASP A 465 -1 N GLY A 463 O THR A 472 SHEET 1 B 8 ILE A 299 TYR A 301 0 SHEET 2 B 8 TRP A 268 VAL A 271 1 N VAL A 271 O ALA A 300 SHEET 3 B 8 VAL A 225 ASP A 229 1 N TYR A 228 O CYS A 270 SHEET 4 B 8 LYS A 129 MET A 134 1 N LEU A 132 O ASP A 229 SHEET 5 B 8 PHE A 91 ILE A 96 1 N ILE A 96 O ASP A 133 SHEET 6 B 8 ARG A 57 THR A 61 1 N PHE A 59 O ARG A 93 SHEET 7 B 8 GLY A 378 TYR A 381 1 O TYR A 381 N ASN A 60 SHEET 8 B 8 ILE A 348 LEU A 349 1 N LEU A 349 O GLY A 378 SHEET 1 C 4 THR A 416 THR A 423 0 SHEET 2 C 4 ARG A 426 GLU A 432 -1 O THR A 430 N GLU A 419 SHEET 3 C 4 VAL A 482 PRO A 488 -1 O VAL A 484 N LEU A 429 SHEET 4 C 4 VAL A 454 GLU A 457 -1 N HIS A 455 O THR A 487 LINK O1 16C A 603 C1 BGC B 1 1555 1555 1.42 LINK O4 BGC B 1 C1 GAL B 2 1555 1555 1.40 LINK O3 GAL B 2 C2 SIA B 3 1555 1555 1.36 LINK O PRO A 69 NA NA A 607 1555 1555 2.21 LINK O ALA A 162 NA NA A 605 1555 1555 2.41 LINK O THR A 165 NA NA A 605 1555 1555 2.46 LINK O ASN A 222 NA NA A 604 1555 1555 2.38 LINK O VAL A 225 NA NA A 604 1555 1555 2.31 LINK O ASP A 291 NA NA A 606 1555 1555 2.30 LINK OE1 GLN A 297 NA NA A 606 1555 1555 2.60 LINK NA NA A 604 O HOH A 696 1555 1555 2.30 LINK NA NA A 604 O HOH A 717 1555 1555 2.46 LINK NA NA A 604 O AHOH A 745 1555 1555 2.40 LINK NA NA A 604 O HOH A 758 1555 1555 2.43 LINK NA NA A 605 O AHOH A 797 1555 1555 2.32 LINK NA NA A 605 O BHOH A 797 1555 1555 2.53 LINK NA NA A 605 O HOH A 923 1555 1555 2.10 LINK NA NA A 605 O HOH A 979 1555 1555 2.45 LINK NA NA A 606 O HOH A 676 1555 1555 2.44 LINK NA NA A 606 O HOH A 847 1555 1555 2.39 LINK NA NA A 606 O HOH A 976 1555 1555 2.31 LINK NA NA A 606 O HOH A 988 1555 1555 2.51 LINK NA NA A 607 O HOH A 671 1555 1555 2.52 LINK NA NA A 607 O HOH A 703 1555 3455 2.60 LINK NA NA A 607 O AHOH A1053 1555 1555 2.38 LINK NA NA A 607 O BHOH A1166 1555 1555 2.46 CISPEP 1 THR A 61 ALA A 62 0 -8.14 CISPEP 2 TRP A 382 SER A 383 0 4.01 CRYST1 77.801 61.984 102.846 90.00 112.25 90.00 C 1 2 1 4 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 0.012853 0.000000 0.005258 0.00000 SCALE2 0.000000 0.016133 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010506 0.00000