HEADER SUGAR BINDING PROTEIN 17-OCT-17 5YLG TITLE CRYSTAL STRUCTURE OF LYSM DOMAIN FROM PTERIS RYUKYUENSIS CHITINASE A COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: LYSM DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PTERIS RYUKYUENSIS; SOURCE 3 ORGANISM_TAXID: 367335; SOURCE 4 GENE: PRCHIA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CBM, CHITINASE, LYSM, PLANT PROTEIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.OHNUMA,Y.KITAOKU,N.UMEMOTO,T.NUMATA,T.FUKAMIZO REVDAT 2 22-NOV-23 5YLG 1 LINK REVDAT 1 24-OCT-18 5YLG 0 JRNL AUTH Y.KITAOKU,N.UMEMOTO,T.TAIRA,T.FUKAMIZO,T.NUMATA,T.OHNUMA JRNL TITL CRYSTAL STRUCTURE OF LYSM DOMAIN FROM PTERIS RYUKYUENSIS JRNL TITL 2 CHITINASE A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 29086 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1544 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) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2047 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.1880 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.1980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1363 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 198 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.11000 REMARK 3 B33 (A**2) : -0.56000 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): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.155 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1414 ; 0.025 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1264 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1933 ; 2.313 ; 1.918 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2911 ; 1.021 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 194 ; 5.655 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;38.069 ;26.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 209 ;11.669 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ;19.177 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 233 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1661 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 317 ; 0.001 ; 0.020 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): 758 ; 1.741 ; 1.391 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 757 ; 1.739 ; 1.389 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 943 ; 2.385 ; 2.077 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 944 ; 2.384 ; 2.079 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 656 ; 2.201 ; 1.530 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 657 ; 2.199 ; 1.532 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 986 ; 3.158 ; 2.224 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1827 ; 4.929 ;12.530 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1828 ; 4.928 ;12.537 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 : 1.20 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 5YLG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30690 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 57.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4PXV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M ZINC ACETATE DIHYDRATE, 25% PEG REMARK 280 3350, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 19.41950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.18100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.06250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.18100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.41950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.06250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 1 REMARK 465 LYS A 49 REMARK 465 MET B 1 REMARK 465 CYS B 2 REMARK 465 MET C 1 REMARK 465 CYS C 2 REMARK 465 LYS C 49 REMARK 465 MET D 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 GLN A 18 CG CD OE1 NE2 REMARK 470 ARG A 20 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 GLN C 18 CG CD OE1 NE2 REMARK 470 ARG D 20 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 38 CG OD1 ND2 REMARK 470 LYS D 49 CG CD CE NZ 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 C SER C 48 O HOH C 239 2.16 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 TYR B 14 CE1 TYR B 14 CZ -0.084 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 A 2 CA - CB - SG ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG B 20 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP B 26 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 GLU B 28 OE1 - CD - OE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ASP D 11 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP D 26 CB - CG - OD2 ANGL. DEV. = -10.1 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 ALA A 32 67.44 26.59 REMARK 500 ASN A 38 41.93 -144.18 REMARK 500 ALA B 32 113.96 -25.93 REMARK 500 ASN B 38 46.54 -148.90 REMARK 500 ASN C 38 57.31 -148.30 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 26 OD2 REMARK 620 2 ASP B 35 OD2 39.9 REMARK 620 3 ASN B 37 OD1 43.6 4.0 REMARK 620 4 GLU C 28 OE1 111.2 103.3 103.9 REMARK 620 5 GLU C 28 OE2 89.9 57.9 56.4 54.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 28 OE1 REMARK 620 2 GLU A 28 OE2 59.3 REMARK 620 3 ASP C 35 OD1 91.9 108.5 REMARK 620 4 ASP C 35 OD2 125.4 89.7 54.1 REMARK 620 5 ASN C 37 OD1 100.5 159.8 70.3 104.4 REMARK 620 6 ASP D 26 OD2 110.5 97.2 152.3 117.6 89.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 35 OD2 REMARK 620 2 ASN A 37 OD1 104.3 REMARK 620 3 ASP B 26 OD1 104.1 105.8 REMARK 620 4 GLU D 28 OE1 111.8 109.6 120.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO D 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PXV RELATED DB: PDB REMARK 900 THE STRUCTURE WAS DETERMINED BY SAD AND AT LOWER RESOLUTION DBREF 5YLG A 2 49 UNP Q0WYK2 Q0WYK2_9MONI 88 135 DBREF 5YLG B 2 49 UNP Q0WYK2 Q0WYK2_9MONI 88 135 DBREF 5YLG C 2 49 UNP Q0WYK2 Q0WYK2_9MONI 88 135 DBREF 5YLG D 2 49 UNP Q0WYK2 Q0WYK2_9MONI 88 135 SEQADV 5YLG MET A 1 UNP Q0WYK2 INITIATING METHIONINE SEQADV 5YLG MET B 1 UNP Q0WYK2 INITIATING METHIONINE SEQADV 5YLG MET C 1 UNP Q0WYK2 INITIATING METHIONINE SEQADV 5YLG MET D 1 UNP Q0WYK2 INITIATING METHIONINE SEQRES 1 A 49 MET CYS THR THR TYR THR ILE LYS SER GLY ASP THR CYS SEQRES 2 A 49 TYR ALA ILE SER GLN ALA ARG GLY ILE SER LEU SER ASP SEQRES 3 A 49 PHE GLU SER TRP ASN ALA GLY ILE ASP CYS ASN ASN LEU SEQRES 4 A 49 GLN ILE GLY GLN VAL VAL CYS VAL SER LYS SEQRES 1 B 49 MET CYS THR THR TYR THR ILE LYS SER GLY ASP THR CYS SEQRES 2 B 49 TYR ALA ILE SER GLN ALA ARG GLY ILE SER LEU SER ASP SEQRES 3 B 49 PHE GLU SER TRP ASN ALA GLY ILE ASP CYS ASN ASN LEU SEQRES 4 B 49 GLN ILE GLY GLN VAL VAL CYS VAL SER LYS SEQRES 1 C 49 MET CYS THR THR TYR THR ILE LYS SER GLY ASP THR CYS SEQRES 2 C 49 TYR ALA ILE SER GLN ALA ARG GLY ILE SER LEU SER ASP SEQRES 3 C 49 PHE GLU SER TRP ASN ALA GLY ILE ASP CYS ASN ASN LEU SEQRES 4 C 49 GLN ILE GLY GLN VAL VAL CYS VAL SER LYS SEQRES 1 D 49 MET CYS THR THR TYR THR ILE LYS SER GLY ASP THR CYS SEQRES 2 D 49 TYR ALA ILE SER GLN ALA ARG GLY ILE SER LEU SER ASP SEQRES 3 D 49 PHE GLU SER TRP ASN ALA GLY ILE ASP CYS ASN ASN LEU SEQRES 4 D 49 GLN ILE GLY GLN VAL VAL CYS VAL SER LYS HET ZN A 101 1 HET ZN A 102 1 HET EDO A 103 4 HET ZN A 104 1 HET EDO D 101 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 ZN 3(ZN 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 10 HOH *198(H2 O) HELIX 1 AA1 THR A 12 GLY A 21 1 10 HELIX 2 AA2 SER A 23 TRP A 30 1 8 HELIX 3 AA3 ASP A 35 LEU A 39 5 5 HELIX 4 AA4 THR B 12 ARG B 20 1 9 HELIX 5 AA5 SER B 23 ASN B 31 1 9 HELIX 6 AA6 ASP B 35 LEU B 39 5 5 HELIX 7 AA7 THR C 12 GLY C 21 1 10 HELIX 8 AA8 SER C 23 TRP C 30 1 8 HELIX 9 AA9 THR D 12 GLY D 21 1 10 HELIX 10 AB1 SER D 23 ASN D 31 1 9 HELIX 11 AB2 ASP D 35 LEU D 39 5 5 SHEET 1 AA1 2 THR A 4 THR A 6 0 SHEET 2 AA1 2 VAL A 44 CYS A 46 -1 O VAL A 45 N TYR A 5 SHEET 1 AA2 2 THR B 4 THR B 6 0 SHEET 2 AA2 2 VAL B 44 CYS B 46 -1 O VAL B 45 N TYR B 5 SHEET 1 AA3 2 THR C 4 THR C 6 0 SHEET 2 AA3 2 VAL C 44 CYS C 46 -1 O VAL C 45 N TYR C 5 SHEET 1 AA4 2 THR D 4 THR D 6 0 SHEET 2 AA4 2 VAL D 44 CYS D 46 -1 O VAL D 45 N TYR D 5 SSBOND 1 CYS A 2 CYS A 46 1555 1555 2.06 SSBOND 2 CYS A 13 CYS A 36 1555 1555 2.18 SSBOND 3 CYS B 13 CYS B 36 1555 1555 2.07 SSBOND 4 CYS C 13 CYS C 36 1555 1555 2.19 SSBOND 5 CYS D 2 CYS D 46 1555 1555 2.08 SSBOND 6 CYS D 13 CYS D 36 1555 1555 2.19 LINK OD2 ASP A 26 ZN ZN A 101 1555 1555 1.87 LINK OE1 GLU A 28 ZN ZN A 104 1555 1555 1.85 LINK OE2 GLU A 28 ZN ZN A 104 1555 1555 2.47 LINK OD2 ASP A 35 ZN ZN A 102 1555 1555 2.06 LINK OD1 ASN A 37 ZN ZN A 102 1555 1555 1.84 LINK ZN ZN A 101 OD2 ASP B 35 2444 1555 2.00 LINK ZN ZN A 101 OD1 ASN B 37 2444 1555 2.04 LINK ZN ZN A 101 OE1 GLU C 28 1555 1555 1.95 LINK ZN ZN A 101 OE2 GLU C 28 1555 1555 2.70 LINK ZN ZN A 102 OD1 ASP B 26 1555 1555 2.04 LINK ZN ZN A 102 OE1 GLU D 28 1555 1555 2.11 LINK ZN ZN A 104 OD1 ASP C 35 1555 1555 2.70 LINK ZN ZN A 104 OD2 ASP C 35 1555 1555 2.02 LINK ZN ZN A 104 OD1 ASN C 37 1555 1555 2.16 LINK ZN ZN A 104 OD2 ASP D 26 1555 1555 2.04 SITE 1 AC1 4 ASP A 26 ASP B 35 ASN B 37 GLU C 28 SITE 1 AC2 4 ASP A 35 ASN A 37 ASP B 26 GLU D 28 SITE 1 AC3 3 SER A 9 GLY A 10 ASP A 11 SITE 1 AC4 4 GLU A 28 ASP C 35 ASN C 37 ASP D 26 SITE 1 AC5 7 TYR B 14 GLY C 42 HOH C 209 ASN D 31 SITE 2 AC5 7 ALA D 32 ILE D 34 HOH D 207 CRYST1 38.839 50.125 92.362 90.00 90.00 90.00 P 21 21 21 16 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 0.025747 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019950 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010827 0.00000