HEADER HYDROLASE 30-JUN-09 3I3L TITLE CRYSTAL STRUCTURE OF CMLS, A FLAVIN-DEPENDENT HALOGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKYLHALIDASE CMLS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES VENEZUELAE; SOURCE 3 ORGANISM_TAXID: 54571; SOURCE 4 GENE: CMLS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS CMLS, FLAVIN-DEPENDENT HALOGENASE, CHLORAMPHENICOL KEYWDS 2 BIOSYNTHESIS, HALOGENATION REACTION, STRUCTURAL GENOMICS, KEYWDS 3 MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS INITIATIVE, KEYWDS 4 BSGI, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.PODZELINSKA,A.SOARES,Z.JIA,MONTREAL-KINGSTON BACTERIAL AUTHOR 2 STRUCTURAL GENOMICS INITIATIVE (BSGI) REVDAT 1 09-MAR-10 3I3L 0 JRNL AUTH K.PODZELINSKA,R.LATIMER,A.BHATTACHARYA,L.C.VINING, JRNL AUTH 2 D.L.ZECHEL,Z.JIA JRNL TITL CHLORAMPHENICOL BIOSYNTHESIS: THE STRUCTURE OF JRNL TITL 2 CMLS, A FLAVIN-DEPENDENT HALOGENASE SHOWING A JRNL TITL 3 COVALENT FLAVIN-ASPARTATE BOND JRNL REF J.MOL.BIOL. V. 397 316 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20080101 JRNL DOI 10.1016/J.JMB.2010.01.020 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 34078 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1786 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2385 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE SET COUNT : 115 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44000 REMARK 3 B22 (A**2) : -1.74000 REMARK 3 B33 (A**2) : 2.17000 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): 0.246 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.154 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.981 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4514 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6113 ; 1.538 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 547 ; 6.930 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;33.946 ;23.170 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 734 ;17.540 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;19.631 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 643 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3487 ; 0.009 ; 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): 2715 ; 1.325 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4342 ; 2.291 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1799 ; 3.443 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1771 ; 5.058 ; 4.500 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 REMARK 3 THE RESIDUES F390, F408, R409, D499, R559, L560 WERE REFINED AS REMARK 3 GLYCINE, AND RESIDUE R481 AS ALANINE, BECAUSE THE SIDE CHAIN REMARK 3 DENSITY WAS NOT OBSERVED FOR THESE RESIDUES. REMARK 4 REMARK 4 3I3L COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUL-09. REMARK 100 THE RCSB ID CODE IS RCSB053920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : CHANNEL-CUT SI(111) CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : VERTICALLY COLLIMATING REMARK 200 MIRROR, DOUBLY FOCUSING REMARK 200 TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36054 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 35.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA HEPES, 19% PEG 3350, PH REMARK 280 7.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 104.04500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.86800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 104.04500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.86800 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: 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 -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 LYS A 93 REMARK 465 VAL A 94 REMARK 465 LEU A 393 REMARK 465 ALA A 394 REMARK 465 GLY A 395 REMARK 465 ASN A 396 REMARK 465 GLY A 397 REMARK 465 PRO A 398 REMARK 465 GLU A 399 REMARK 465 ASP A 400 REMARK 465 PRO A 401 REMARK 465 SER A 402 REMARK 465 GLY A 403 REMARK 465 THR A 404 REMARK 465 VAL A 405 REMARK 465 ALA A 406 REMARK 465 SER A 407 REMARK 465 VAL A 567 REMARK 465 GLU A 568 REMARK 465 TYR A 569 REMARK 465 GLU A 570 REMARK 465 VAL A 571 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 PHE A 390 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 PHE A 408 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 409 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG A 481 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 499 CB CG OD1 OD2 REMARK 470 ARG A 559 CB CG CD NE CZ NH1 NH2 REMARK 470 LEU A 560 CB CG CD1 CD2 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 LYS A 258 CE LYS A 258 NZ 0.153 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 ASP A 380 CB - CG - OD1 ANGL. DEV. = 5.7 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 SER A 73 -177.42 -174.03 REMARK 500 ALA A 90 129.12 -36.92 REMARK 500 ALA A 91 137.15 -171.48 REMARK 500 ALA A 102 -153.44 -137.33 REMARK 500 ARG A 184 79.72 -115.54 REMARK 500 ALA A 266 154.48 -44.42 REMARK 500 ASP A 281 -152.96 -118.87 REMARK 500 ASP A 288 -114.50 51.60 REMARK 500 LYS A 387 48.08 -70.36 REMARK 500 PHE A 390 -12.95 -44.95 REMARK 500 GLU A 391 50.21 -142.07 REMARK 500 PHE A 513 170.05 -59.55 REMARK 500 ARG A 559 -141.89 -90.11 REMARK 500 LEU A 560 42.19 93.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 387 LYS A 388 139.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 386 24.3 L L OUTSIDE RANGE REMARK 500 PHE A 562 25.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 600 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHORS STATE THAT THE CMLS SEQUENCE DEPOSITED IN DATABASE IS REMARK 999 INCORRECT AND THE NATURALLY OCCURING PROTEIN DOES NOT ACTUALLY REMARK 999 HAVE THESE RESIDUES. SO RESIDUES ILE 303 - VAL 308 ARE NOT REMARK 999 PRESENT IN THE CRYSTAL DBREF 3I3L A 1 571 UNP Q9AL91 Q9AL91_9ACTO 1 577 SEQADV 3I3L MET A -19 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L GLY A -18 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L SER A -17 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L SER A -16 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -15 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -14 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -13 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -12 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -11 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A -10 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L SER A -9 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L SER A -8 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L GLY A -7 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L LEU A -6 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L VAL A -5 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L PRO A -4 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L ARG A -3 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L GLY A -2 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L SER A -1 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L HIS A 0 UNP Q9AL91 EXPRESSION TAG SEQADV 3I3L A UNP Q9AL91 ILE 303 SEE REMARK 999 SEQADV 3I3L A UNP Q9AL91 PHE 304 SEE REMARK 999 SEQADV 3I3L A UNP Q9AL91 ARG 305 SEE REMARK 999 SEQADV 3I3L A UNP Q9AL91 ARG 306 SEE REMARK 999 SEQADV 3I3L A UNP Q9AL91 SER 307 SEE REMARK 999 SEQADV 3I3L A UNP Q9AL91 VAL 308 SEE REMARK 999 SEQRES 1 A 591 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 591 LEU VAL PRO ARG GLY SER HIS MET THR ARG SER LYS VAL SEQRES 3 A 591 ALA ILE ILE GLY GLY GLY PRO ALA GLY SER VAL ALA GLY SEQRES 4 A 591 LEU THR LEU HIS LYS LEU GLY HIS ASP VAL THR ILE TYR SEQRES 5 A 591 GLU ARG SER ALA PHE PRO ARG TYR ARG VAL GLY GLU SER SEQRES 6 A 591 LEU LEU PRO GLY THR MET SER ILE LEU ASN ARG LEU GLY SEQRES 7 A 591 LEU GLN GLU LYS ILE ASP ALA GLN ASN TYR VAL LYS LYS SEQRES 8 A 591 PRO SER ALA THR PHE LEU TRP GLY GLN ASP GLN ALA PRO SEQRES 9 A 591 TRP THR PHE SER PHE ALA ALA PRO LYS VAL ALA PRO TRP SEQRES 10 A 591 VAL PHE ASP HIS ALA VAL GLN VAL LYS ARG GLU GLU PHE SEQRES 11 A 591 ASP LYS LEU LEU LEU ASP GLU ALA ARG SER ARG GLY ILE SEQRES 12 A 591 THR VAL HIS GLU GLU THR PRO VAL THR ASP VAL ASP LEU SEQRES 13 A 591 SER ASP PRO ASP ARG VAL VAL LEU THR VAL ARG ARG GLY SEQRES 14 A 591 GLY GLU SER VAL THR VAL GLU SER ASP PHE VAL ILE ASP SEQRES 15 A 591 ALA GLY GLY SER GLY GLY PRO ILE SER ARG LYS LEU GLY SEQRES 16 A 591 VAL ARG GLN TYR ASP GLU PHE TYR ARG ASN PHE ALA VAL SEQRES 17 A 591 TRP SER TYR PHE LYS LEU LYS ASP PRO PHE GLU GLY ASP SEQRES 18 A 591 LEU LYS GLY THR THR TYR SER ILE THR PHE GLU ASP GLY SEQRES 19 A 591 TRP VAL TRP MET ILE PRO ILE LYS ASP ASP LEU TYR SER SEQRES 20 A 591 VAL GLY LEU VAL VAL ASP ARG SER LYS SER ALA GLU VAL SEQRES 21 A 591 ARG GLU GLN GLY ALA ASP ALA PHE TYR SER SER THR LEU SEQRES 22 A 591 ALA LYS CYS ALA LYS ALA MET ASP ILE LEU GLY GLY ALA SEQRES 23 A 591 GLU GLN VAL ASP GLU VAL ARG ILE VAL GLN ASP TRP SER SEQRES 24 A 591 TYR ASP THR GLU VAL PHE SER ALA ASP ARG PHE PHE LEU SEQRES 25 A 591 CYS GLY ASP ALA ALA CYS PHE THR ASP PRO LEU PHE SER SEQRES 26 A 591 GLN GLY VAL HIS LEU ALA SER GLN SER ALA VAL SER ALA SEQRES 27 A 591 ALA ALA ALA ILE ASP ARG ILE THR ARG HIS GLY ASP GLU SEQRES 28 A 591 LYS ASP ALA VAL HIS ALA TRP TYR ASN ARG THR TYR ARG SEQRES 29 A 591 GLU ALA TYR GLU GLN TYR HIS GLN PHE LEU ALA SER PHE SEQRES 30 A 591 TYR THR PHE ALA SER PHE THR GLU PRO ASP SER GLU PHE SEQRES 31 A 591 TRP ARG LYS ARG ARG ILE THR GLU SER ASP ASP ASP ARG SEQRES 32 A 591 LEU THR ARG LYS LYS TRP PHE GLU SER LEU ALA GLY ASN SEQRES 33 A 591 GLY PRO GLU ASP PRO SER GLY THR VAL ALA SER PHE ARG SEQRES 34 A 591 ASP ARG ALA SER THR MET ILE ALA ILE GLY ARG HIS GLN SEQRES 35 A 591 ARG PRO GLU LEU SER ASP ASP PHE SER GLU ALA GLU LEU SEQRES 36 A 591 ASN PRO ALA ARG VAL ARG TRP ILE SER ASP LEU THR LYS SEQRES 37 A 591 ARG LEU ASN SER ILE THR ARG PHE LYS TRP THR GLY GLY SEQRES 38 A 591 LYS ALA VAL LEU LYS GLN HIS TYR ARG VAL GLU PRO ILE SEQRES 39 A 591 GLY PHE ARG LEU GLU GLN ARG GLU VAL LEU ALA ASN GLY SEQRES 40 A 591 GLU GLY LEU ASP MET ALA GLN TYR PRO MET ASP ASP GLU SEQRES 41 A 591 ALA ARG GLN ILE PHE GLN ASP LEU ALA GLU GLU GLU PHE SEQRES 42 A 591 GLY TYR LYS THR LEU VAL LYS ARG LEU GLY ALA VAL GLY SEQRES 43 A 591 ARG GLN GLU LEU SER THR GLN ILE VAL VAL ARG LEU MET SEQRES 44 A 591 GLU ALA GLY LEU LEU THR GLY TYR ASP ALA GLN GLY GLU SEQRES 45 A 591 LYS VAL PHE VAL GLN GLY ARG LEU HIS PHE GLY GLY VAL SEQRES 46 A 591 GLY VAL GLU TYR GLU VAL HET FAD A 600 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 HOH *232(H2 O) HELIX 1 1 GLY A 12 LEU A 25 1 14 HELIX 2 2 LEU A 47 LEU A 57 1 11 HELIX 3 3 LEU A 59 ASN A 67 1 9 HELIX 4 4 LYS A 106 ARG A 121 1 16 HELIX 5 5 GLY A 164 GLY A 167 5 4 HELIX 6 6 GLY A 168 GLY A 175 1 8 HELIX 7 7 LYS A 236 GLY A 244 1 9 HELIX 8 8 GLY A 244 ALA A 254 1 11 HELIX 9 9 CYS A 256 GLY A 264 1 9 HELIX 10 10 GLY A 294 ALA A 297 5 4 HELIX 11 11 ASP A 301 SER A 305 5 5 HELIX 12 12 GLN A 306 HIS A 328 1 23 HELIX 13 13 GLU A 331 PHE A 363 1 33 HELIX 14 14 SER A 368 ARG A 375 1 8 HELIX 15 15 SER A 379 LYS A 387 1 9 HELIX 16 16 LYS A 388 SER A 392 5 5 HELIX 17 18 SER A 431 GLU A 434 5 4 HELIX 18 19 LEU A 435 SER A 452 1 18 HELIX 19 20 ASP A 498 GLU A 512 1 15 HELIX 20 21 GLY A 514 ALA A 524 1 11 HELIX 21 22 LEU A 530 ALA A 541 1 12 SHEET 1 A 6 THR A 124 HIS A 126 0 SHEET 2 A 6 ASP A 28 TYR A 32 1 N ILE A 31 O HIS A 126 SHEET 3 A 6 LYS A 5 ILE A 9 1 N VAL A 6 O ASP A 28 SHEET 4 A 6 PHE A 159 ASP A 162 1 O ILE A 161 N ILE A 9 SHEET 5 A 6 PHE A 290 LEU A 292 1 O PHE A 291 N ASP A 162 SHEET 6 A 6 SER A 286 ALA A 287 -1 N ALA A 287 O PHE A 290 SHEET 1 B 2 VAL A 69 LYS A 71 0 SHEET 2 B 2 ALA A 102 GLN A 104 -1 O ALA A 102 N LYS A 71 SHEET 1 C 7 TRP A 85 SER A 88 0 SHEET 2 C 7 SER A 73 LEU A 77 -1 N PHE A 76 O TRP A 85 SHEET 3 C 7 THR A 206 PHE A 211 1 O SER A 208 N LEU A 77 SHEET 4 C 7 GLY A 214 PRO A 220 -1 O VAL A 216 N ILE A 209 SHEET 5 C 7 LEU A 225 ASP A 233 -1 O VAL A 231 N TRP A 215 SHEET 6 C 7 ARG A 177 LYS A 193 -1 N VAL A 188 O LEU A 230 SHEET 7 C 7 GLU A 267 GLN A 268 -1 O GLU A 267 N LYS A 193 SHEET 1 D 7 TRP A 85 SER A 88 0 SHEET 2 D 7 SER A 73 LEU A 77 -1 N PHE A 76 O TRP A 85 SHEET 3 D 7 THR A 206 PHE A 211 1 O SER A 208 N LEU A 77 SHEET 4 D 7 GLY A 214 PRO A 220 -1 O VAL A 216 N ILE A 209 SHEET 5 D 7 LEU A 225 ASP A 233 -1 O VAL A 231 N TRP A 215 SHEET 6 D 7 ARG A 177 LYS A 193 -1 N VAL A 188 O LEU A 230 SHEET 7 D 7 ARG A 273 THR A 282 -1 O VAL A 275 N ALA A 187 SHEET 1 E 3 VAL A 131 ASP A 135 0 SHEET 2 E 3 VAL A 142 ARG A 148 -1 O THR A 145 N ASP A 133 SHEET 3 E 3 GLU A 151 SER A 157 -1 O VAL A 153 N VAL A 146 SHEET 1 F 3 ILE A 453 TRP A 458 0 SHEET 2 F 3 LEU A 544 ASP A 548 -1 O THR A 545 N LYS A 457 SHEET 3 F 3 LYS A 553 VAL A 554 -1 O VAL A 554 N GLY A 546 SHEET 1 G 3 ALA A 463 VAL A 471 0 SHEET 2 G 3 LEU A 478 ASN A 486 -1 O ALA A 485 N VAL A 464 SHEET 3 G 3 ASP A 491 MET A 492 -1 O MET A 492 N LEU A 484 LINK OD1 ASP A 277 C8M FAD A 600 1555 1555 1.45 CISPEP 1 PHE A 37 PRO A 38 0 2.11 SITE 1 AC1 33 GLY A 10 GLY A 12 PRO A 13 ALA A 14 SITE 2 AC1 33 TYR A 32 GLU A 33 ARG A 34 SER A 35 SITE 3 AC1 33 ARG A 39 ARG A 41 VAL A 42 GLY A 43 SITE 4 AC1 33 GLU A 44 SER A 45 ARG A 107 PRO A 130 SITE 5 AC1 33 VAL A 131 ALA A 163 GLY A 164 GLY A 165 SITE 6 AC1 33 ALA A 187 ASP A 277 GLY A 294 ASP A 295 SITE 7 AC1 33 SER A 305 GLY A 307 VAL A 308 HOH A 572 SITE 8 AC1 33 HOH A 574 HOH A 587 HOH A 589 HOH A 635 SITE 9 AC1 33 HOH A 738 CRYST1 208.090 57.736 59.883 90.00 97.47 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 0.004806 0.000000 0.000630 0.00000 SCALE2 0.000000 0.017320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016842 0.00000