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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
