HEADER TRANSFERASE 03-FEB-18 6CBM TITLE X-RAY STRUCTURE OF NEOB FROM STREPTOMYCES FRADIAE IN COMPLEX WITH PLP TITLE 2 AND NEOMYCIN (AS THE EXTERNAL ALDIMINE) AT PH 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEAMINE TRANSAMINASE NEON; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLUTAMATE--6'-DEHYDROPAROMAMINE AMINOTRANSFERASE,NEOMYCIN C COMPND 5 TRANSAMINASE,NEOMYCIN BIOSYNTHESIS PROTEIN 18,NEO-18,NEOMYCIN COMPND 6 BIOSYNTHESIS PROTEIN B,NEOMYCIN BIOSYNTHESIS PROTEIN N; COMPND 7 EC: 2.6.1.93,2.6.1.95; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES FRADIAE; SOURCE 3 ORGANISM_TAXID: 1906; SOURCE 4 GENE: NEON, NEO18, NEOB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEOMYCIN, AMINOTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.B.THODEN,G.T.DOW,H.M.HOLDEN REVDAT 6 04-OCT-23 6CBM 1 REMARK REVDAT 5 01-JAN-20 6CBM 1 REMARK REVDAT 4 09-MAY-18 6CBM 1 JRNL REVDAT 3 21-MAR-18 6CBM 1 JRNL REVDAT 2 28-FEB-18 6CBM 1 REMARK REVDAT 1 21-FEB-18 6CBM 0 JRNL AUTH G.T.DOW,J.B.THODEN,H.M.HOLDEN JRNL TITL THE THREE-DIMENSIONAL STRUCTURE OF NEOB: AN AMINOTRANSFERASE JRNL TITL 2 INVOLVED IN THE BIOSYNTHESIS OF NEOMYCIN. JRNL REF PROTEIN SCI. V. 27 945 2018 JRNL REFN ESSN 1469-896X JRNL PMID 29516565 JRNL DOI 10.1002/PRO.3400 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0124 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 91161 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 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 : 4781 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6044 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 320 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6192 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 124 REMARK 3 SOLVENT ATOMS : 808 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.22000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : -0.54000 REMARK 3 B13 (A**2) : -0.68000 REMARK 3 B23 (A**2) : 0.47000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.093 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.095 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.227 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6511 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6187 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8880 ; 1.600 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14152 ; 0.812 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 831 ; 6.426 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 292 ;31.919 ;21.849 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 956 ;15.078 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 78 ;16.504 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 995 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7412 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1528 ; 0.000 ; 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): 3286 ; 2.263 ; 1.702 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3285 ; 2.260 ; 1.701 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4108 ; 2.864 ; 2.544 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4109 ; 2.865 ; 2.545 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3225 ; 3.770 ; 2.141 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3225 ; 3.770 ; 2.141 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4765 ; 5.400 ; 3.056 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8313 ; 6.668 ;15.657 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8314 ; 6.668 ;15.660 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 : NULL 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 6CBM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95942 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.24800 REMARK 200 R SYM FOR SHELL (I) : 0.24800 REMARK 200 FOR SHELL : 2.700 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: 6CBK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-20% PEG-3350, 100 MM MGCL2, 100 MM REMARK 280 CHES, 1 MMPLP, 5 MM NEOMYCIN, PH 9, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL 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 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 GLU A -9 REMARK 465 ASN A -8 REMARK 465 LEU A -7 REMARK 465 TYR A -6 REMARK 465 PHE A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 ASN A 4 REMARK 465 SER A 5 REMARK 465 ASP A 415 REMARK 465 ASP A 416 REMARK 465 MET B -21 REMARK 465 GLY B -20 REMARK 465 SER B -19 REMARK 465 SER B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 SER B -11 REMARK 465 SER B -10 REMARK 465 GLU B -9 REMARK 465 ASN B -8 REMARK 465 LEU B -7 REMARK 465 TYR B -6 REMARK 465 PHE B -5 REMARK 465 GLN B -4 REMARK 465 GLY B -3 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 LYS B 3 REMARK 465 ASN B 4 REMARK 465 SER B 5 REMARK 465 ASP B 415 REMARK 465 ASP B 416 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 B 902 O HOH B 946 1.73 REMARK 500 NZ LYS B 250 O HOH B 601 2.04 REMARK 500 NH1 ARG B 191 O HOH B 602 2.06 REMARK 500 O HOH A 605 O HOH A 635 2.17 REMARK 500 O HOH A 924 O HOH A 972 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 942 O HOH B 805 1556 2.08 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 116 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 116 NE - CZ - NH2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 363 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 116 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 116 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 412 NE - CZ - NH2 ANGL. DEV. = -3.0 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 ASP A 57 118.17 -37.28 REMARK 500 LEU A 143 -0.29 72.09 REMARK 500 ALA A 166 69.80 -117.24 REMARK 500 LEU A 210 -2.71 76.54 REMARK 500 ALA A 230 -55.36 -165.82 REMARK 500 ALA A 234 23.44 -150.52 REMARK 500 ASP A 344 -154.51 -114.48 REMARK 500 ALA B 166 76.85 -115.88 REMARK 500 ALA B 230 -53.36 -164.33 REMARK 500 ALA B 234 24.93 -149.33 REMARK 500 ASP B 344 -152.63 -115.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1013 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH B 995 DISTANCE = 6.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OZY A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OZY B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 504 DBREF 6CBM A 1 416 UNP Q53U08 NEON_STRFR 1 416 DBREF 6CBM B 1 416 UNP Q53U08 NEON_STRFR 1 416 SEQADV 6CBM MET A -21 UNP Q53U08 INITIATING METHIONINE SEQADV 6CBM GLY A -20 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER A -19 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER A -18 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -17 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -16 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -15 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -14 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -13 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A -12 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER A -11 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER A -10 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLU A -9 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM ASN A -8 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM LEU A -7 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM TYR A -6 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM PHE A -5 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLN A -4 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY A -3 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY A -2 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY A -1 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS A 0 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM MET B -21 UNP Q53U08 INITIATING METHIONINE SEQADV 6CBM GLY B -20 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER B -19 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER B -18 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -17 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -16 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -15 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -14 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -13 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B -12 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER B -11 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM SER B -10 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLU B -9 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM ASN B -8 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM LEU B -7 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM TYR B -6 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM PHE B -5 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLN B -4 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY B -3 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY B -2 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM GLY B -1 UNP Q53U08 EXPRESSION TAG SEQADV 6CBM HIS B 0 UNP Q53U08 EXPRESSION TAG SEQRES 1 A 438 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLU SEQRES 2 A 438 ASN LEU TYR PHE GLN GLY GLY GLY HIS MET THR LYS ASN SEQRES 3 A 438 SER SER LEU LEU ALA GLU PHE PRO THR CYS PRO ARG ASP SEQRES 4 A 438 GLU LYS ASP ARG PRO ARG VAL PHE THR ALA ALA SER GLY SEQRES 5 A 438 ALA TRP LEU THR ASP GLU SER GLY PHE ARG TRP ILE ASP SEQRES 6 A 438 PHE ASP ASN ALA ARG GLY SER ILE LEU LEU GLY HIS GLY SEQRES 7 A 438 ASP PRO VAL VAL ALA GLU ALA VAL ALA ARG ALA ALA THR SEQRES 8 A 438 GLY ALA ASP GLY THR ALA THR GLY TRP SER ARG ARG VAL SEQRES 9 A 438 ASP ALA VAL LEU GLU ARG LEU HIS ALA LEU CYS GLY GLY SEQRES 10 A 438 GLU VAL VAL GLY LEU PHE ARG SER GLY THR ALA ALA VAL SEQRES 11 A 438 ARG ALA ALA VAL LEU ALA VAL ARG GLU ALA THR GLY ARG SEQRES 12 A 438 PRO LEU LEU LEU SER ALA GLY TYR HIS GLY TYR ASP PRO SEQRES 13 A 438 MET TRP TYR PRO SER GLU ALA PRO LEU GLU PRO ASN ALA SEQRES 14 A 438 ASP GLY VAL VAL ASP PHE PHE PHE ASP LEU GLY LEU LEU SEQRES 15 A 438 ARG GLU LEU LEU ARG ALA PRO GLU ARG VAL ALA ALA VAL SEQRES 16 A 438 VAL VAL SER PRO ASP HIS MET HIS LEU SER PRO GLY TRP SEQRES 17 A 438 TYR ARG GLU LEU ARG ARG LEU CYS SER ALA ALA GLY VAL SEQRES 18 A 438 VAL LEU VAL ALA ASP GLU VAL LYS VAL GLY LEU ARG TYR SEQRES 19 A 438 ALA PRO GLY LEU SER THR ALA GLU LEU LEU ALA PRO ASP SEQRES 20 A 438 VAL TRP VAL VAL ALA LYS GLY MET ALA ASN GLY HIS ALA SEQRES 21 A 438 VAL SER ALA VAL GLY GLY SER ARG ARG LEU LEU LYS PRO SEQRES 22 A 438 LEU LYS GLU VAL SER PHE THR SER PHE PHE GLU PRO THR SEQRES 23 A 438 ILE LEU ALA ALA ALA ASP ALA ALA LEU ALA ARG VAL ALA SEQRES 24 A 438 THR GLY GLU PRO GLN ARG ALA VAL ARG GLU ALA GLY ASP SEQRES 25 A 438 ARG PHE LEU ARG HIS ALA ARG LYS ALA LEU ASP ASP ALA SEQRES 26 A 438 SER LEU PRO VAL GLU ILE ALA GLY ASP GLY THR PHE PHE SEQRES 27 A 438 GLN PHE VAL PRO ALA THR GLU GLU LEU GLU GLU ALA LEU SEQRES 28 A 438 TYR GLY ALA ALA ASN ALA GLU GLY LEU LEU PHE TYR ALA SEQRES 29 A 438 GLY ASP ASN GLN GLY VAL SER ALA ALA PHE ASP GLU ALA SEQRES 30 A 438 VAL LEU GLY GLU ALA GLU ARG ARG PHE ALA ARG VAL CYS SEQRES 31 A 438 GLU ARG LEU ALA PRO TYR ALA GLY GLY GLU PRO VAL GLY SEQRES 32 A 438 ASP ALA ALA ARG TYR ARG VAL ALA TRP ASN VAL MET ASP SEQRES 33 A 438 GLY LEU ARG GLN ALA PRO ARG ASP ARG GLU GLU THR THR SEQRES 34 A 438 GLY LEU LEU ALA ARG LEU LEU ASP ASP SEQRES 1 B 438 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLU SEQRES 2 B 438 ASN LEU TYR PHE GLN GLY GLY GLY HIS MET THR LYS ASN SEQRES 3 B 438 SER SER LEU LEU ALA GLU PHE PRO THR CYS PRO ARG ASP SEQRES 4 B 438 GLU LYS ASP ARG PRO ARG VAL PHE THR ALA ALA SER GLY SEQRES 5 B 438 ALA TRP LEU THR ASP GLU SER GLY PHE ARG TRP ILE ASP SEQRES 6 B 438 PHE ASP ASN ALA ARG GLY SER ILE LEU LEU GLY HIS GLY SEQRES 7 B 438 ASP PRO VAL VAL ALA GLU ALA VAL ALA ARG ALA ALA THR SEQRES 8 B 438 GLY ALA ASP GLY THR ALA THR GLY TRP SER ARG ARG VAL SEQRES 9 B 438 ASP ALA VAL LEU GLU ARG LEU HIS ALA LEU CYS GLY GLY SEQRES 10 B 438 GLU VAL VAL GLY LEU PHE ARG SER GLY THR ALA ALA VAL SEQRES 11 B 438 ARG ALA ALA VAL LEU ALA VAL ARG GLU ALA THR GLY ARG SEQRES 12 B 438 PRO LEU LEU LEU SER ALA GLY TYR HIS GLY TYR ASP PRO SEQRES 13 B 438 MET TRP TYR PRO SER GLU ALA PRO LEU GLU PRO ASN ALA SEQRES 14 B 438 ASP GLY VAL VAL ASP PHE PHE PHE ASP LEU GLY LEU LEU SEQRES 15 B 438 ARG GLU LEU LEU ARG ALA PRO GLU ARG VAL ALA ALA VAL SEQRES 16 B 438 VAL VAL SER PRO ASP HIS MET HIS LEU SER PRO GLY TRP SEQRES 17 B 438 TYR ARG GLU LEU ARG ARG LEU CYS SER ALA ALA GLY VAL SEQRES 18 B 438 VAL LEU VAL ALA ASP GLU VAL LYS VAL GLY LEU ARG TYR SEQRES 19 B 438 ALA PRO GLY LEU SER THR ALA GLU LEU LEU ALA PRO ASP SEQRES 20 B 438 VAL TRP VAL VAL ALA LYS GLY MET ALA ASN GLY HIS ALA SEQRES 21 B 438 VAL SER ALA VAL GLY GLY SER ARG ARG LEU LEU LYS PRO SEQRES 22 B 438 LEU LYS GLU VAL SER PHE THR SER PHE PHE GLU PRO THR SEQRES 23 B 438 ILE LEU ALA ALA ALA ASP ALA ALA LEU ALA ARG VAL ALA SEQRES 24 B 438 THR GLY GLU PRO GLN ARG ALA VAL ARG GLU ALA GLY ASP SEQRES 25 B 438 ARG PHE LEU ARG HIS ALA ARG LYS ALA LEU ASP ASP ALA SEQRES 26 B 438 SER LEU PRO VAL GLU ILE ALA GLY ASP GLY THR PHE PHE SEQRES 27 B 438 GLN PHE VAL PRO ALA THR GLU GLU LEU GLU GLU ALA LEU SEQRES 28 B 438 TYR GLY ALA ALA ASN ALA GLU GLY LEU LEU PHE TYR ALA SEQRES 29 B 438 GLY ASP ASN GLN GLY VAL SER ALA ALA PHE ASP GLU ALA SEQRES 30 B 438 VAL LEU GLY GLU ALA GLU ARG ARG PHE ALA ARG VAL CYS SEQRES 31 B 438 GLU ARG LEU ALA PRO TYR ALA GLY GLY GLU PRO VAL GLY SEQRES 32 B 438 ASP ALA ALA ARG TYR ARG VAL ALA TRP ASN VAL MET ASP SEQRES 33 B 438 GLY LEU ARG GLN ALA PRO ARG ASP ARG GLU GLU THR THR SEQRES 34 B 438 GLY LEU LEU ALA ARG LEU LEU ASP ASP HET OZY A 501 57 HET EDO A 502 4 HET OZY B 501 57 HET EDO B 502 4 HET CL B 503 1 HET CL B 504 1 HETNAM OZY (1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(3-O-{2-AMINO-2,6- HETNAM 2 OZY DIDEOXY-6-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY) HETNAM 3 OZY METHYL]PYRIDIN-4-YL}METHYL)AMINO]-ALPHA-D- HETNAM 4 OZY GLUCOPYRANOSYL}-BETA-D-RIBOFURANOSYL)OXY]-3- HETNAM 5 OZY HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D- HETNAM 6 OZY GLUCOPYRANOSIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 OZY 2(C31 H56 N7 O18 P) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *808(H2 O) HELIX 1 AA1 ASP A 45 SER A 50 1 6 HELIX 2 AA2 ASP A 57 THR A 69 1 13 HELIX 3 AA3 SER A 79 GLY A 94 1 16 HELIX 4 AA4 SER A 103 GLY A 120 1 18 HELIX 5 AA5 ASP A 133 TYR A 137 5 5 HELIX 6 AA6 ASP A 156 LEU A 164 1 9 HELIX 7 AA7 ARG A 165 GLU A 168 5 4 HELIX 8 AA8 SER A 183 GLY A 198 1 16 HELIX 9 AA9 LEU A 249 VAL A 255 5 7 HELIX 10 AB1 GLU A 262 THR A 278 1 17 HELIX 11 AB2 GLY A 279 ALA A 303 1 25 HELIX 12 AB3 THR A 322 GLU A 336 1 15 HELIX 13 AB4 ASP A 353 LEU A 371 1 19 HELIX 14 AB5 ALA A 372 ALA A 375 5 4 HELIX 15 AB6 GLY A 381 ASP A 394 1 14 HELIX 16 AB7 ASP A 402 LEU A 414 1 13 HELIX 17 AB8 ASP B 45 SER B 50 1 6 HELIX 18 AB9 ASP B 57 THR B 69 1 13 HELIX 19 AC1 SER B 79 GLY B 94 1 16 HELIX 20 AC2 SER B 103 GLY B 120 1 18 HELIX 21 AC3 ASP B 133 TYR B 137 5 5 HELIX 22 AC4 ASP B 156 LEU B 164 1 9 HELIX 23 AC5 ARG B 165 GLU B 168 5 4 HELIX 24 AC6 SER B 183 GLY B 198 1 16 HELIX 25 AC7 LEU B 249 VAL B 255 5 7 HELIX 26 AC8 GLU B 262 THR B 278 1 17 HELIX 27 AC9 GLY B 279 ALA B 303 1 25 HELIX 28 AD1 THR B 322 GLU B 336 1 15 HELIX 29 AD2 ASP B 353 LEU B 371 1 19 HELIX 30 AD3 ALA B 372 ALA B 375 5 4 HELIX 31 AD4 GLY B 381 ASP B 394 1 14 HELIX 32 AD5 ASP B 402 LEU B 414 1 13 SHEET 1 AA1 4 PHE A 25 SER A 29 0 SHEET 2 AA1 4 TRP A 32 ASP A 35 -1 O TRP A 32 N SER A 29 SHEET 3 AA1 4 ARG A 40 ASP A 43 -1 O TRP A 41 N LEU A 33 SHEET 4 AA1 4 LEU A 338 LEU A 339 1 O LEU A 339 N ILE A 42 SHEET 1 AA2 7 VAL A 97 PHE A 101 0 SHEET 2 AA2 7 SER A 240 GLY A 244 -1 O VAL A 242 N GLY A 99 SHEET 3 AA2 7 VAL A 226 VAL A 229 -1 N VAL A 229 O ALA A 241 SHEET 4 AA2 7 VAL A 200 GLU A 205 1 N ALA A 203 O VAL A 226 SHEET 5 AA2 7 VAL A 170 VAL A 175 1 N VAL A 173 O VAL A 202 SHEET 6 AA2 7 LEU A 123 ALA A 127 1 N LEU A 125 O VAL A 174 SHEET 7 AA2 7 VAL A 150 ASP A 152 1 O VAL A 151 N LEU A 124 SHEET 1 AA3 2 VAL A 307 GLY A 311 0 SHEET 2 AA3 2 PHE A 316 PRO A 320 -1 O VAL A 319 N GLU A 308 SHEET 1 AA4 4 PHE B 25 SER B 29 0 SHEET 2 AA4 4 TRP B 32 ASP B 35 -1 O THR B 34 N ALA B 27 SHEET 3 AA4 4 ARG B 40 ASP B 43 -1 O TRP B 41 N LEU B 33 SHEET 4 AA4 4 LEU B 338 LEU B 339 1 O LEU B 339 N ILE B 42 SHEET 1 AA5 7 VAL B 97 PHE B 101 0 SHEET 2 AA5 7 SER B 240 GLY B 244 -1 O VAL B 242 N GLY B 99 SHEET 3 AA5 7 VAL B 226 VAL B 229 -1 N VAL B 229 O ALA B 241 SHEET 4 AA5 7 VAL B 200 GLU B 205 1 N ALA B 203 O VAL B 226 SHEET 5 AA5 7 VAL B 170 VAL B 175 1 N VAL B 173 O VAL B 202 SHEET 6 AA5 7 LEU B 123 ALA B 127 1 N LEU B 125 O VAL B 174 SHEET 7 AA5 7 VAL B 150 ASP B 152 1 O VAL B 151 N LEU B 124 SHEET 1 AA6 2 VAL B 307 GLY B 311 0 SHEET 2 AA6 2 PHE B 316 PRO B 320 -1 O VAL B 319 N GLU B 308 SITE 1 AC1 30 THR A 13 ARG A 48 GLY A 104 THR A 105 SITE 2 AC1 30 TYR A 129 HIS A 130 GLY A 131 SER A 176 SITE 3 AC1 30 ASP A 204 VAL A 206 LYS A 207 LYS A 231 SITE 4 AC1 30 ASP A 344 ASN A 391 VAL A 392 ASP A 394 SITE 5 AC1 30 HOH A 610 HOH A 644 HOH A 661 HOH A 663 SITE 6 AC1 30 HOH A 675 HOH A 688 HOH A 690 HOH A 692 SITE 7 AC1 30 HOH A 774 HOH A 859 GLU B 254 SER B 256 SITE 8 AC1 30 PHE B 257 THR B 258 SITE 1 AC2 6 ASP A 156 ARG A 401 ASP A 402 ARG A 403 SITE 2 AC2 6 THR A 406 HOH A 748 SITE 1 AC3 33 GLU A 254 SER A 256 PHE A 257 THR A 258 SITE 2 AC3 33 HOH A 739 HOH A 925 THR B 13 ARG B 48 SITE 3 AC3 33 GLY B 104 THR B 105 TYR B 129 HIS B 130 SITE 4 AC3 33 GLY B 131 SER B 176 ASP B 204 VAL B 206 SITE 5 AC3 33 LYS B 207 LYS B 231 TYR B 341 ASP B 344 SITE 6 AC3 33 ASN B 391 VAL B 392 ASP B 394 HOH B 604 SITE 7 AC3 33 HOH B 605 HOH B 633 HOH B 641 HOH B 687 SITE 8 AC3 33 HOH B 691 HOH B 720 HOH B 744 HOH B 748 SITE 9 AC3 33 HOH B 836 SITE 1 AC4 12 ARG A 102 SER A 103 ALA A 106 TYR A 132 SITE 2 AC4 12 ARG B 102 SER B 103 ALA B 106 TYR B 132 SITE 3 AC4 12 HOH B 635 HOH B 737 HOH B 754 HOH B 789 SITE 1 AC5 4 PHE B 155 LEU B 157 TRP B 186 HOH B 859 SITE 1 AC6 2 ALA B 384 ARG B 387 CRYST1 57.742 59.153 70.313 69.58 77.62 78.45 P 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 0.017318 -0.003539 -0.002818 0.00000 SCALE2 0.000000 0.017255 -0.005822 0.00000 SCALE3 0.000000 0.000000 0.015367 0.00000