PDB Short entry for 3RLG HEADER HYDROLASE 19-APR-11 3RLG TITLE CRYSTAL STRUCTURE OF LOXOSCELES INTERMEDIA PHOSPHOLIPASE D ISOFORM 1 TITLE 2 H12A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPHINGOMYELIN PHOSPHODIESTERASE D LISICTOX-ALPHAIA1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DERMONECROTIC PROTEIN 1, LIRECDT1, SPHINGOMYELIN COMPND 5 PHOSPHODIESTERASE D 1, SMD 1, SMASE D 1, SPHINGOMYELINASE D 1; COMPND 6 EC: 3.1.4.41; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LOXOSCELES INTERMEDIA; SOURCE 3 ORGANISM_COMMON: SPIDER; SOURCE 4 ORGANISM_TAXID: 58218; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-14B KEYWDS TIM BETA/ALPHA-BARREL, PLC-LIKE PHOSPHODIESTERASE, INACTIVE MUTANT KEYWDS 2 H12A PHOSPHOLIPASE D, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.O.GIUSEPPE,A.ULLAH,S.S.VEIGA,M.T.MURAKAMI,R.K.ARNI REVDAT 2 13-SEP-23 3RLG 1 REMARK SEQADV LINK REVDAT 1 24-AUG-11 3RLG 0 JRNL AUTH A.ULLAH,P.O.DE GIUSEPPE,M.T.MURAKAMI,D.TREVISAN-SILVA, JRNL AUTH 2 A.C.WILLE,D.CHAVES-MOREIRA,L.H.GREMSKI,R.B.DA SILVEIRA, JRNL AUTH 3 A.SENNF-RIBEIRO,O.M.CHAIM,S.S.VEIGA,R.K.ARNI JRNL TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS JRNL TITL 2 OF A CLASS II PHOSPHOLIPASE D FROM LOXOSCELES INTERMEDIA JRNL TITL 3 VENOM. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 234 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21301094 JRNL DOI 10.1107/S1744309110050931 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 32820 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1730 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) : 2042 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.4020 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.4040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2183 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 51 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.16000 REMARK 3 B33 (A**2) : -0.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.04000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.089 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.610 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2309 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3123 ; 2.133 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 291 ; 6.188 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;36.177 ;24.831 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 363 ;12.136 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;15.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 330 ; 0.166 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1785 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1395 ; 1.382 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2243 ; 2.175 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 914 ; 3.226 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 872 ; 4.840 ; 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 3RLG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000065077. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.458 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 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) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.37000 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: MOLREP REMARK 200 STARTING MODEL: 3RLH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 7.5 AND 35%(V/V) REMARK 280 PEG200 , VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.72750 REMARK 290 SMTRY3 2 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: PISA 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 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 PRO A -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 MET A -1 REMARK 465 LEU A 0 REMARK 465 GLU A 1 REMARK 465 LYS A 285 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 LYS A 58 CD CE NZ REMARK 480 LYS A 59 CD CE NZ REMARK 480 LYS A 84 CD CE NZ REMARK 480 LYS A 184 CG CD CE NZ REMARK 480 LYS A 234 CD CE NZ REMARK 480 LYS A 269 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CG2 THR A 189 OD2 ASP A 276 2546 2.05 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 PHE A 90 CD1 PHE A 90 CE1 0.124 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 4 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 4 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLY A 167 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 ASP A 276 CB - CG - OD1 ANGL. DEV. = 6.5 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 GLU A 43 -61.91 -123.10 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 A 286 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 32 OE2 REMARK 620 2 ASP A 34 OD1 98.1 REMARK 620 3 ASP A 91 OD2 96.2 87.5 REMARK 620 4 HOH A 357 O 84.9 79.2 166.7 REMARK 620 5 HOH A 475 O 163.1 98.6 87.0 95.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 289 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 290 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 291 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 292 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 293 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 294 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RLH RELATED DB: PDB DBREF 3RLG A 2 285 UNP P0CE80 A1HA_LOXIN 28 306 SEQADV 3RLG MET A -21 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG GLY A -20 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG SER A -19 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG SER A -18 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -17 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -16 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -15 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -14 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -13 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -12 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG SER A -11 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG SER A -10 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG GLY A -9 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG LEU A -8 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG VAL A -7 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG PRO A -6 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG ARG A -5 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG GLY A -4 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG SER A -3 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG HIS A -2 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG MET A -1 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG LEU A 0 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG GLU A 1 UNP P0CE80 EXPRESSION TAG SEQADV 3RLG ALA A 12 UNP P0CE80 HIS 38 ENGINEERED MUTATION SEQADV 3RLG ASP A 277 UNP P0CE80 GLU 298 CLONING ARTIFACT SEQRES 1 A 302 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 302 LEU VAL PRO ARG GLY SER HIS MET LEU GLU GLY ASN ARG SEQRES 3 A 302 ARG PRO ILE TRP ILE MET GLY ALA MET VAL ASN ALA ILE SEQRES 4 A 302 GLY GLN ILE ASP GLU PHE VAL ASN LEU GLY ALA ASN SER SEQRES 5 A 302 ILE GLU THR ASP VAL SER PHE ASP ASP ASN ALA ASN PRO SEQRES 6 A 302 GLU TYR THR TYR HIS GLY ILE PRO CYS ASP CYS GLY ARG SEQRES 7 A 302 ASN CYS LYS LYS TYR GLU ASN PHE ASN ASP PHE LEU LYS SEQRES 8 A 302 GLY LEU ARG SER ALA THR THR PRO GLY ASN SER LYS TYR SEQRES 9 A 302 GLN GLU LYS LEU VAL LEU VAL VAL PHE ASP LEU LYS THR SEQRES 10 A 302 GLY SER LEU TYR ASP ASN GLN ALA ASN ASP ALA GLY LYS SEQRES 11 A 302 LYS LEU ALA LYS ASN LEU LEU GLN HIS TYR TRP ASN ASN SEQRES 12 A 302 GLY ASN ASN GLY GLY ARG ALA TYR ILE VAL LEU SER ILE SEQRES 13 A 302 PRO ASP LEU ASN HIS TYR PRO LEU ILE LYS GLY PHE LYS SEQRES 14 A 302 ASP GLN LEU THR LYS ASP GLY HIS PRO GLU LEU MET ASP SEQRES 15 A 302 LYS VAL GLY HIS ASP PHE SER GLY ASN ASP ASP ILE GLY SEQRES 16 A 302 ASP VAL GLY LYS ALA TYR LYS LYS ALA GLY ILE THR GLY SEQRES 17 A 302 HIS ILE TRP GLN SER ASP GLY ILE THR ASN CYS LEU PRO SEQRES 18 A 302 ARG GLY LEU SER ARG VAL ASN ALA ALA VAL ALA ASN ARG SEQRES 19 A 302 ASP SER ALA ASN GLY PHE ILE ASN LYS VAL TYR TYR TRP SEQRES 20 A 302 THR VAL ASP LYS ARG SER THR THR ARG ASP ALA LEU ASP SEQRES 21 A 302 ALA GLY VAL ASP GLY ILE MET THR ASN TYR PRO ASP VAL SEQRES 22 A 302 ILE THR ASP VAL LEU ASN GLU ALA ALA TYR LYS LYS LYS SEQRES 23 A 302 PHE ARG VAL ALA THR TYR ASP ASP ASN PRO TRP VAL THR SEQRES 24 A 302 PHE LYS LYS HET MG A 286 1 HET EDO A 287 4 HET PEG A 288 7 HET PGE A 289 10 HET EDO A 290 4 HET EDO A 291 4 HET PGE A 292 10 HET PEG A 293 7 HET EDO A 294 4 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MG MG 2+ FORMUL 3 EDO 4(C2 H6 O2) FORMUL 4 PEG 2(C4 H10 O3) FORMUL 5 PGE 2(C6 H14 O4) FORMUL 11 HOH *238(H2 O) HELIX 1 1 GLY A 18 LEU A 26 1 9 HELIX 2 2 ASN A 62 THR A 75 1 14 HELIX 3 3 THR A 94 LEU A 97 5 4 HELIX 4 4 TYR A 98 ASN A 100 5 3 HELIX 5 5 GLN A 101 TYR A 117 1 17 HELIX 6 6 TRP A 118 ASN A 122 5 5 HELIX 7 7 ASP A 135 HIS A 138 5 4 HELIX 8 8 TYR A 139 ASP A 152 1 14 HELIX 9 9 HIS A 154 ASP A 159 5 6 HELIX 10 10 ASP A 175 ALA A 186 1 12 HELIX 11 11 LEU A 207 ASP A 218 1 12 HELIX 12 12 LYS A 234 ALA A 244 1 11 HELIX 13 13 TYR A 253 ASN A 262 1 10 HELIX 14 14 GLU A 263 LYS A 268 1 6 SHEET 1 A 8 VAL A 161 PHE A 165 0 SHEET 2 A 8 TYR A 128 ILE A 133 1 N ILE A 133 O ASP A 164 SHEET 3 A 8 LEU A 87 LEU A 92 1 N PHE A 90 O VAL A 130 SHEET 4 A 8 SER A 30 VAL A 35 1 N THR A 33 O ASP A 91 SHEET 5 A 8 ARG A 5 GLY A 11 1 N GLY A 11 O SER A 30 SHEET 6 A 8 GLY A 248 THR A 251 1 O ILE A 249 N MET A 10 SHEET 7 A 8 LYS A 226 TRP A 230 1 N TYR A 229 O MET A 250 SHEET 8 A 8 TRP A 193 GLY A 197 1 N GLN A 194 O TYR A 228 SHEET 1 B 6 VAL A 161 PHE A 165 0 SHEET 2 B 6 TYR A 128 ILE A 133 1 N ILE A 133 O ASP A 164 SHEET 3 B 6 LEU A 87 LEU A 92 1 N PHE A 90 O VAL A 130 SHEET 4 B 6 SER A 30 VAL A 35 1 N THR A 33 O ASP A 91 SHEET 5 B 6 ARG A 5 GLY A 11 1 N GLY A 11 O SER A 30 SHEET 6 B 6 PHE A 270 VAL A 272 1 O ARG A 271 N ILE A 7 SSBOND 1 CYS A 51 CYS A 57 1555 1555 2.00 SSBOND 2 CYS A 53 CYS A 201 1555 1555 2.09 LINK OE2 GLU A 32 MG MG A 286 1555 1555 2.15 LINK OD1 ASP A 34 MG MG A 286 1555 1555 2.24 LINK OD2 ASP A 91 MG MG A 286 1555 1555 2.26 LINK MG MG A 286 O HOH A 357 1555 1555 2.32 LINK MG MG A 286 O HOH A 475 1555 1555 2.27 CISPEP 1 ILE A 49 PRO A 50 0 2.53 CISPEP 2 TRP A 230 THR A 231 0 -19.27 SITE 1 AC1 5 GLU A 32 ASP A 34 ASP A 91 HOH A 357 SITE 2 AC1 5 HOH A 475 SITE 1 AC2 1 ASN A 200 SITE 1 AC3 3 ASN A 41 LYS A 108 PGE A 289 SITE 1 AC4 5 ASP A 104 LYS A 107 LYS A 108 LYS A 111 SITE 2 AC4 5 PEG A 288 SITE 1 AC5 2 ASN A 137 LYS A 185 SITE 1 AC6 3 ASP A 39 ASN A 39A HOH A 387 SITE 1 AC7 2 ALA A 264 LYS A 268 SITE 1 AC8 1 LYS A 267 SITE 1 AC9 3 GLY A 180 ILE A 188 PHE A 223 CRYST1 49.575 49.455 56.395 90.00 105.56 90.00 P 1 21 1 2 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 0.020171 0.000000 0.005617 0.00000 SCALE2 0.000000 0.020220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018407 0.00000