HEADER HYDROLASE 12-APR-07 2UYR TITLE CRYSTAL STRUCTURE OF BACILLUS CEREUS SPHINGOMYELINASE MUTANT :N57A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOMYELINASE C; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: SPHINGOMYELINASE, SPHINGOMYELIN PHOSPHODIESTERASE, SMASE, COMPND 5 SMPLC, CEREOLYSIN B; COMPND 6 EC: 3.1.4.12; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS; SOURCE 3 ORGANISM_TAXID: 1396; SOURCE 4 STRAIN: IAM 1029; SOURCE 5 VARIANT: N57A; SOURCE 6 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PHY300PLK KEYWDS HYDROLASE, N57A METAL ION OF SIDE-EDGE, BACILLUS CEREUS KEYWDS 2 SPHINGOMYELINASE, HEMOLYSIS, CYTOLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR M.ODA,H.TSUGE,J.SAKURAI REVDAT 5 16-OCT-24 2UYR 1 REMARK REVDAT 4 13-DEC-23 2UYR 1 LINK REVDAT 3 04-APR-18 2UYR 1 REMARK REVDAT 2 24-FEB-09 2UYR 1 VERSN REVDAT 1 27-MAY-08 2UYR 0 JRNL AUTH M.ODA,H.TSUGE,J.SAKURAI JRNL TITL CRYSTAL STRUCTURE OF BACILLUS CEREUS SPHINGOMYELINASE MUTANT JRNL TITL 2 : N57A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 13721 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 724 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 955 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2361 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 89 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : -0.68000 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): 0.352 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.243 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.142 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2419 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 7 ; 0.059 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3293 ; 1.631 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13 ; 0.761 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 298 ; 7.175 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;41.539 ;25.862 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 398 ;17.718 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;19.305 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 358 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1878 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 7 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 873 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6 ; 0.228 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1620 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 10 ; 0.274 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 131 ; 0.145 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.023 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.224 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.356 ; 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): 1521 ; 1.139 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 5 ; 0.106 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2420 ; 2.046 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1040 ; 2.710 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 873 ; 4.141 ; 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 : 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 2UYR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-07. REMARK 100 THE DEPOSITION ID IS D_1290032256. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGING PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4I REMARK 200 STARTING MODEL: PDB ENTRY 2DDT REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CALCIUM ACETATE 0.2 M SODIUM REMARK 280 CACODYLATE (PH7.5) 18% PEG 8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 27.54500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.84500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.96350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.84500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.54500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.96350 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN X, ASN 84 TO ALA 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 GLU X 1 REMARK 465 ALA X 2 REMARK 465 SER X 3 REMARK 465 THR X 4 REMARK 465 THR X 5 REMARK 465 GLN X 6 REMARK 465 LYS X 306 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 O HOH X 2075 O HOH X 2076 2.06 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 CYS X 123 CB CYS X 123 SG -0.152 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 CYS X 123 CA - CB - SG ANGL. DEV. = 10.5 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 MET X 19 67.19 -105.50 REMARK 500 ASN X 27 42.89 -102.96 REMARK 500 LEU X 78 121.72 -36.38 REMARK 500 ASN X 130 30.12 89.46 REMARK 500 ASP X 142 -10.32 69.93 REMARK 500 HIS X 261 -157.80 -134.70 REMARK 500 PHE X 285 -17.07 86.66 REMARK 500 REMARK 500 REMARK: NULL 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 MG X1306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU X 53 OE1 REMARK 620 2 HOH X2009 O 90.8 REMARK 620 3 HOH X2010 O 98.8 95.5 REMARK 620 4 HOH X2083 O 76.8 96.2 167.5 REMARK 620 5 HOH X2084 O 162.3 99.1 94.8 87.6 REMARK 620 6 HOH X2086 O 85.5 175.9 86.9 81.1 84.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG X1306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DDR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH REMARK 900 CALCIUM ION REMARK 900 RELATED ID: 2DDS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH REMARK 900 COBALT ION REMARK 900 RELATED ID: 2DDT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SPHINGOMYELINASE FROM BACILLUS CEREUSWITH REMARK 900 MAGNESIUM ION DBREF 2UYR X 1 306 UNP P11889 PHL2_BACCE 28 333 SEQADV 2UYR ALA X 57 UNP P11889 ASN 84 ENGINEERED MUTATION SEQADV 2UYR HIS X 296 UNP P11889 ASP 323 CONFLICT SEQRES 1 X 306 GLU ALA SER THR THR GLN ASN ASP THR LEU LYS VAL MET SEQRES 2 X 306 THR HIS ASN VAL TYR MET LEU SER THR ASN LEU TYR PRO SEQRES 3 X 306 ASN TRP GLY GLN THR GLU ARG ALA ASP LEU ILE GLY ALA SEQRES 4 X 306 ALA ASP TYR ILE LYS ASN GLN ASP VAL VAL ILE LEU ASN SEQRES 5 X 306 GLU VAL PHE ASP ALA SER ALA SER ASP ARG LEU LEU GLY SEQRES 6 X 306 ASN LEU LYS LYS GLU TYR PRO ASN GLN THR ALA VAL LEU SEQRES 7 X 306 GLY ARG SER SER GLY SER GLU TRP ASP LYS THR LEU GLY SEQRES 8 X 306 ASN TYR SER SER SER THR PRO GLU ASP GLY GLY VAL ALA SEQRES 9 X 306 ILE VAL SER LYS TRP PRO ILE ALA GLU LYS ILE GLN TYR SEQRES 10 X 306 VAL PHE ALA LYS GLY CYS GLY PRO ASP ASN LEU SER ASN SEQRES 11 X 306 LYS GLY PHE VAL TYR THR LYS ILE LYS LYS ASN ASP ARG SEQRES 12 X 306 PHE VAL HIS VAL ILE GLY THR HIS LEU GLN ALA GLU ASP SEQRES 13 X 306 SER MET CYS GLY LYS THR SER PRO ALA SER VAL ARG THR SEQRES 14 X 306 ASN GLN LEU LYS GLU ILE GLN ASP PHE ILE LYS ASN LYS SEQRES 15 X 306 ASN ILE PRO ASN ASN GLU TYR VAL LEU ILE GLY GLY ASP SEQRES 16 X 306 MET ASN VAL ASN LYS ILE ASN ALA GLU ASN ASN ASN ASP SEQRES 17 X 306 SER GLU TYR ALA SER MET PHE LYS THR LEU ASN ALA SER SEQRES 18 X 306 VAL PRO SER TYR THR GLY HIS THR ALA THR TRP ASP ALA SEQRES 19 X 306 THR THR ASN SER ILE ALA LYS TYR ASN PHE PRO ASP SER SEQRES 20 X 306 PRO ALA GLU TYR LEU ASP TYR ILE ILE ALA SER LYS ASP SEQRES 21 X 306 HIS ALA ASN PRO SER TYR ILE GLU ASN LYS VAL LEU GLN SEQRES 22 X 306 PRO LYS SER PRO GLN TRP THR VAL THR SER TRP PHE GLN SEQRES 23 X 306 LYS TYR THR TYR ASN ASP TYR SER ASP HIS TYR PRO VAL SEQRES 24 X 306 GLU ALA THR ILE SER MET LYS HET MG X1306 1 HETNAM MG MAGNESIUM ION FORMUL 2 MG MG 2+ FORMUL 3 HOH *89(H2 O) HELIX 1 1 GLY X 29 ALA X 39 1 11 HELIX 2 2 ASP X 56 LYS X 68 1 13 HELIX 3 3 CYS X 123 SER X 129 5 7 HELIX 4 4 ASP X 156 GLY X 160 5 5 HELIX 5 5 SER X 163 ASN X 181 1 19 HELIX 6 6 SER X 209 ASN X 219 1 11 HELIX 7 7 ASN X 237 PHE X 244 1 8 SHEET 1 XA 7 ASN X 73 GLN X 74 0 SHEET 2 XA 7 ALA X 104 SER X 107 -1 O SER X 107 N ASN X 73 SHEET 3 XA 7 VAL X 48 VAL X 54 -1 O VAL X 49 N VAL X 106 SHEET 4 XA 7 THR X 9 MET X 19 1 O MET X 13 N ILE X 50 SHEET 5 XA 7 VAL X 299 SER X 304 -1 O VAL X 299 N THR X 14 SHEET 6 XA 7 TYR X 266 VAL X 271 -1 O TYR X 266 N SER X 304 SHEET 7 XA 7 SER X 224 GLY X 227 1 O SER X 224 N ASN X 269 SHEET 1 XB 6 LYS X 88 GLY X 91 0 SHEET 2 XB 6 ILE X 111 VAL X 118 1 O GLN X 116 N LEU X 90 SHEET 3 XB 6 GLY X 132 LYS X 140 -1 O PHE X 133 N TYR X 117 SHEET 4 XB 6 ARG X 143 HIS X 151 -1 O ARG X 143 N LYS X 140 SHEET 5 XB 6 TYR X 189 ASP X 195 1 O TYR X 189 N HIS X 146 SHEET 6 XB 6 ASP X 253 ALA X 257 -1 O TYR X 254 N GLY X 194 SHEET 1 XC 2 TRP X 279 SER X 283 0 SHEET 2 XC 2 GLN X 286 TYR X 290 -1 O GLN X 286 N SER X 283 SSBOND 1 CYS X 123 CYS X 159 1555 1555 2.01 LINK OE1 GLU X 53 MG MG X1306 1555 1555 2.31 LINK MG MG X1306 O HOH X2009 1555 1555 2.11 LINK MG MG X1306 O HOH X2010 1555 1555 2.07 LINK MG MG X1306 O HOH X2083 1555 1555 2.18 LINK MG MG X1306 O HOH X2084 1555 1555 1.97 LINK MG MG X1306 O HOH X2086 1555 1555 2.08 SITE 1 AC1 6 GLU X 53 HOH X2009 HOH X2010 HOH X2083 SITE 2 AC1 6 HOH X2084 HOH X2086 CRYST1 55.090 63.927 101.690 90.00 90.00 90.00 P 21 21 21 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 0.018152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015643 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009834 0.00000