HEADER LYASE 14-NOV-08 3F9T TITLE CRYSTAL STRUCTURE OF L-TYROSINE DECARBOXYLASE MFNA (EC 4.1.1.25) TITLE 2 (NP_247014.1) FROM METHANOCOCCUS JANNASCHII AT 2.11 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-TYROSINE DECARBOXYLASE MFNA; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TDC; COMPND 5 EC: 4.1.1.25; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 GENE: MFNA, MJ0050, NP_247014.1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS NP_247014.1, L-TYROSINE DECARBOXYLASE MFNA (EC 4.1.1.25), STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN KEYWDS 3 STRUCTURE INITIATIVE, PSI-2, DECARBOXYLASE, LYASE, PYRIDOXAL KEYWDS 4 PHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 01-FEB-23 3F9T 1 REMARK SEQADV REVDAT 5 24-JUL-19 3F9T 1 REMARK LINK REVDAT 4 01-NOV-17 3F9T 1 REMARK REVDAT 3 13-JUL-11 3F9T 1 VERSN REVDAT 2 24-FEB-09 3F9T 1 VERSN REVDAT 1 25-NOV-08 3F9T 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF L-TYROSINE DECARBOXYLASE MFNA (EC JRNL TITL 2 4.1.1.25) (NP_247014.1) FROM METHANOCOCCUS JANNASCHII AT JRNL TITL 3 2.11 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 62056 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3141 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) : 2.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4323 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 214 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6252 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 402 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : 0.32000 REMARK 3 B33 (A**2) : 0.23000 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): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.099 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.222 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6479 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4518 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8741 ; 1.579 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11056 ; 0.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 800 ; 3.776 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 291 ;30.837 ;24.364 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1232 ;11.985 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.516 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 973 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7068 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1260 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1311 ; 0.199 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4663 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3085 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3146 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 363 ; 0.156 ; 0.200 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): 9 ; 0.187 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.290 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.137 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 4391 ; 2.062 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1614 ; 0.615 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6350 ; 2.585 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2801 ; 5.080 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2383 ; 6.466 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 394 4 REMARK 3 1 B 3 B 394 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 5258 ; 0.300 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 5258 ; 1.070 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 394 REMARK 3 ORIGIN FOR THE GROUP (A): 49.7059 85.1569 26.3326 REMARK 3 T TENSOR REMARK 3 T11: 0.0034 T22: -0.0830 REMARK 3 T33: -0.0308 T12: -0.0099 REMARK 3 T13: 0.0981 T23: 0.0227 REMARK 3 L TENSOR REMARK 3 L11: 1.3792 L22: 1.1363 REMARK 3 L33: 1.3055 L12: -0.0533 REMARK 3 L13: -0.5225 L23: 0.1727 REMARK 3 S TENSOR REMARK 3 S11: 0.0761 S12: 0.1591 S13: 0.1812 REMARK 3 S21: -0.3850 S22: 0.0746 S23: -0.2231 REMARK 3 S31: -0.1498 S32: 0.1221 S33: -0.1507 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 394 REMARK 3 ORIGIN FOR THE GROUP (A): 35.9672 83.6177 51.0066 REMARK 3 T TENSOR REMARK 3 T11: -0.1505 T22: -0.0892 REMARK 3 T33: -0.1013 T12: 0.0048 REMARK 3 T13: 0.0259 T23: 0.0364 REMARK 3 L TENSOR REMARK 3 L11: 0.7903 L22: 0.7292 REMARK 3 L33: 0.9293 L12: -0.1192 REMARK 3 L13: -0.0601 L23: -0.1433 REMARK 3 S TENSOR REMARK 3 S11: 0.0176 S12: -0.1094 S13: -0.0293 REMARK 3 S21: -0.0377 S22: 0.0501 S23: 0.0272 REMARK 3 S31: -0.0454 S32: -0.0345 S33: -0.0678 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: 1.HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.2,4- REMARK 3 METHYL PENTANEDIOL (MPD) FROM THE CRYSTALLIZATION CONDITION HAS REMARK 3 BEEN MODELED IN THE SOLVENT STRUCTURE. 5.PYRIDOXAL PHOSPHATE REMARK 3 (PLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE OF BOTH REMARK 3 PROTOMERS BASED ON CLEAR AND UNAMBIGUOUS ELECTRON DENSITY IN THE REMARK 3 EXPERIMENTALLY PHASED MAPS. REMARK 4 REMARK 4 3F9T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97952 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMETER REMARK 200 OPTICS : ADJUSTABLE FOCUSING MIRRORS IN K REMARK 200 -B GEOMETRY REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62121 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 29.975 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : 0.11900 REMARK 200 FOR THE DATA SET : 3.2030 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.77200 REMARK 200 R SYM FOR SHELL (I) : 0.77200 REMARK 200 FOR SHELL : 1.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40.0000% MPD, 0.1M HEPES PH 7.0, REMARK 280 NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 42.63800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.95750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.06400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.95750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.63800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.06400 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 300 REMARK: AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC REMARK 300 ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS FORMING A DIMER. CRYSTAL REMARK 300 PACKING ANALYSIS SUGGESTS THAT THIS IS THE STABLE OLIGOMERIC FORM REMARK 300 IN SOLUTION. 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: 12310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -83.0 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 GLY A 0 REMARK 465 ARG A 395 REMARK 465 ASP A 396 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 ARG B 2 REMARK 465 ARG B 395 REMARK 465 ASP B 396 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 84 CG CD CE NZ REMARK 470 LYS A 197 CD CE NZ REMARK 470 LYS A 224 CD CE NZ REMARK 470 LYS A 353 CD CE NZ REMARK 470 LYS A 368 CE NZ REMARK 470 LYS B 84 CG CD CE NZ REMARK 470 LYS B 119 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 ND2 ASN B 227 O HOH B 535 2.18 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 54 49.86 -89.30 REMARK 500 PHE A 230 -4.40 -145.61 REMARK 500 LYS A 245 -101.52 -93.06 REMARK 500 LEU A 337 -165.40 -110.28 REMARK 500 ASP A 346 52.78 -97.55 REMARK 500 GLU B 54 56.46 -92.71 REMARK 500 VAL B 91 -164.74 -103.61 REMARK 500 VAL B 213 -53.86 -120.06 REMARK 500 PHE B 230 -6.21 -151.50 REMARK 500 LYS B 245 -103.09 -96.64 REMARK 500 LEU B 337 -165.44 -112.24 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 PLP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 397 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 398 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 390948 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3F9T A 1 396 UNP Q60358 MFNA_METJA 1 396 DBREF 3F9T B 1 396 UNP Q60358 MFNA_METJA 1 396 SEQADV 3F9T GLY A 0 UNP Q60358 EXPRESSION TAG SEQADV 3F9T GLY B 0 UNP Q60358 EXPRESSION TAG SEQRES 1 A 397 GLY MSE ARG ASN MSE GLN GLU LYS GLY VAL SER GLU LYS SEQRES 2 A 397 GLU ILE LEU GLU GLU LEU LYS LYS TYR ARG SER LEU ASP SEQRES 3 A 397 LEU LYS TYR GLU ASP GLY ASN ILE PHE GLY SER MSE CYS SEQRES 4 A 397 SER ASN VAL LEU PRO ILE THR ARG LYS ILE VAL ASP ILE SEQRES 5 A 397 PHE LEU GLU THR ASN LEU GLY ASP PRO GLY LEU PHE LYS SEQRES 6 A 397 GLY THR LYS LEU LEU GLU GLU LYS ALA VAL ALA LEU LEU SEQRES 7 A 397 GLY SER LEU LEU ASN ASN LYS ASP ALA TYR GLY HIS ILE SEQRES 8 A 397 VAL SER GLY GLY THR GLU ALA ASN LEU MSE ALA LEU ARG SEQRES 9 A 397 CYS ILE LYS ASN ILE TRP ARG GLU LYS ARG ARG LYS GLY SEQRES 10 A 397 LEU SER LYS ASN GLU HIS PRO LYS ILE ILE VAL PRO ILE SEQRES 11 A 397 THR ALA HIS PHE SER PHE GLU LYS GLY ARG GLU MSE MSE SEQRES 12 A 397 ASP LEU GLU TYR ILE TYR ALA PRO ILE LYS GLU ASP TYR SEQRES 13 A 397 THR ILE ASP GLU LYS PHE VAL LYS ASP ALA VAL GLU ASP SEQRES 14 A 397 TYR ASP VAL ASP GLY ILE ILE GLY ILE ALA GLY THR THR SEQRES 15 A 397 GLU LEU GLY THR ILE ASP ASN ILE GLU GLU LEU SER LYS SEQRES 16 A 397 ILE ALA LYS GLU ASN ASN ILE TYR ILE HIS VAL ASP ALA SEQRES 17 A 397 ALA PHE GLY GLY LEU VAL ILE PRO PHE LEU ASP ASP LYS SEQRES 18 A 397 TYR LYS LYS LYS GLY VAL ASN TYR LYS PHE ASP PHE SER SEQRES 19 A 397 LEU GLY VAL ASP SER ILE THR ILE ASP PRO HIS LYS MSE SEQRES 20 A 397 GLY HIS CYS PRO ILE PRO SER GLY GLY ILE LEU PHE LYS SEQRES 21 A 397 ASP ILE GLY TYR LYS ARG TYR LEU ASP VAL ASP ALA PRO SEQRES 22 A 397 TYR LEU THR GLU THR ARG GLN ALA THR ILE LEU GLY THR SEQRES 23 A 397 ARG VAL GLY PHE GLY GLY ALA CYS THR TYR ALA VAL LEU SEQRES 24 A 397 ARG TYR LEU GLY ARG GLU GLY GLN ARG LYS ILE VAL ASN SEQRES 25 A 397 GLU CYS MSE GLU ASN THR LEU TYR LEU TYR LYS LYS LEU SEQRES 26 A 397 LYS GLU ASN ASN PHE LYS PRO VAL ILE GLU PRO ILE LEU SEQRES 27 A 397 ASN ILE VAL ALA ILE GLU ASP GLU ASP TYR LYS GLU VAL SEQRES 28 A 397 CYS LYS LYS LEU ARG ASP ARG GLY ILE TYR VAL SER VAL SEQRES 29 A 397 CYS ASN CYS VAL LYS ALA LEU ARG ILE VAL VAL MSE PRO SEQRES 30 A 397 HIS ILE LYS ARG GLU HIS ILE ASP ASN PHE ILE GLU ILE SEQRES 31 A 397 LEU ASN SER ILE LYS ARG ASP SEQRES 1 B 397 GLY MSE ARG ASN MSE GLN GLU LYS GLY VAL SER GLU LYS SEQRES 2 B 397 GLU ILE LEU GLU GLU LEU LYS LYS TYR ARG SER LEU ASP SEQRES 3 B 397 LEU LYS TYR GLU ASP GLY ASN ILE PHE GLY SER MSE CYS SEQRES 4 B 397 SER ASN VAL LEU PRO ILE THR ARG LYS ILE VAL ASP ILE SEQRES 5 B 397 PHE LEU GLU THR ASN LEU GLY ASP PRO GLY LEU PHE LYS SEQRES 6 B 397 GLY THR LYS LEU LEU GLU GLU LYS ALA VAL ALA LEU LEU SEQRES 7 B 397 GLY SER LEU LEU ASN ASN LYS ASP ALA TYR GLY HIS ILE SEQRES 8 B 397 VAL SER GLY GLY THR GLU ALA ASN LEU MSE ALA LEU ARG SEQRES 9 B 397 CYS ILE LYS ASN ILE TRP ARG GLU LYS ARG ARG LYS GLY SEQRES 10 B 397 LEU SER LYS ASN GLU HIS PRO LYS ILE ILE VAL PRO ILE SEQRES 11 B 397 THR ALA HIS PHE SER PHE GLU LYS GLY ARG GLU MSE MSE SEQRES 12 B 397 ASP LEU GLU TYR ILE TYR ALA PRO ILE LYS GLU ASP TYR SEQRES 13 B 397 THR ILE ASP GLU LYS PHE VAL LYS ASP ALA VAL GLU ASP SEQRES 14 B 397 TYR ASP VAL ASP GLY ILE ILE GLY ILE ALA GLY THR THR SEQRES 15 B 397 GLU LEU GLY THR ILE ASP ASN ILE GLU GLU LEU SER LYS SEQRES 16 B 397 ILE ALA LYS GLU ASN ASN ILE TYR ILE HIS VAL ASP ALA SEQRES 17 B 397 ALA PHE GLY GLY LEU VAL ILE PRO PHE LEU ASP ASP LYS SEQRES 18 B 397 TYR LYS LYS LYS GLY VAL ASN TYR LYS PHE ASP PHE SER SEQRES 19 B 397 LEU GLY VAL ASP SER ILE THR ILE ASP PRO HIS LYS MSE SEQRES 20 B 397 GLY HIS CYS PRO ILE PRO SER GLY GLY ILE LEU PHE LYS SEQRES 21 B 397 ASP ILE GLY TYR LYS ARG TYR LEU ASP VAL ASP ALA PRO SEQRES 22 B 397 TYR LEU THR GLU THR ARG GLN ALA THR ILE LEU GLY THR SEQRES 23 B 397 ARG VAL GLY PHE GLY GLY ALA CYS THR TYR ALA VAL LEU SEQRES 24 B 397 ARG TYR LEU GLY ARG GLU GLY GLN ARG LYS ILE VAL ASN SEQRES 25 B 397 GLU CYS MSE GLU ASN THR LEU TYR LEU TYR LYS LYS LEU SEQRES 26 B 397 LYS GLU ASN ASN PHE LYS PRO VAL ILE GLU PRO ILE LEU SEQRES 27 B 397 ASN ILE VAL ALA ILE GLU ASP GLU ASP TYR LYS GLU VAL SEQRES 28 B 397 CYS LYS LYS LEU ARG ASP ARG GLY ILE TYR VAL SER VAL SEQRES 29 B 397 CYS ASN CYS VAL LYS ALA LEU ARG ILE VAL VAL MSE PRO SEQRES 30 B 397 HIS ILE LYS ARG GLU HIS ILE ASP ASN PHE ILE GLU ILE SEQRES 31 B 397 LEU ASN SER ILE LYS ARG ASP MODRES 3F9T MSE A 1 MET SELENOMETHIONINE MODRES 3F9T MSE A 4 MET SELENOMETHIONINE MODRES 3F9T MSE A 37 MET SELENOMETHIONINE MODRES 3F9T MSE A 100 MET SELENOMETHIONINE MODRES 3F9T MSE A 141 MET SELENOMETHIONINE MODRES 3F9T MSE A 142 MET SELENOMETHIONINE MODRES 3F9T MSE A 246 MET SELENOMETHIONINE MODRES 3F9T MSE A 314 MET SELENOMETHIONINE MODRES 3F9T MSE A 375 MET SELENOMETHIONINE MODRES 3F9T MSE B 4 MET SELENOMETHIONINE MODRES 3F9T MSE B 37 MET SELENOMETHIONINE MODRES 3F9T MSE B 100 MET SELENOMETHIONINE MODRES 3F9T MSE B 141 MET SELENOMETHIONINE MODRES 3F9T MSE B 142 MET SELENOMETHIONINE MODRES 3F9T MSE B 246 MET SELENOMETHIONINE MODRES 3F9T MSE B 314 MET SELENOMETHIONINE MODRES 3F9T MSE B 375 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 4 8 HET MSE A 37 8 HET MSE A 100 8 HET MSE A 141 8 HET MSE A 142 8 HET MSE A 246 8 HET MSE A 314 8 HET MSE A 375 8 HET MSE B 4 8 HET MSE B 37 8 HET MSE B 100 8 HET MSE B 141 8 HET MSE B 142 8 HET MSE B 246 8 HET MSE B 314 8 HET MSE B 375 8 HET PLP A 500 16 HET MPD A 397 8 HET MPD A 398 8 HET PLP B 500 16 HET MPD B 397 8 HETNAM MSE SELENOMETHIONINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 MSE 17(C5 H11 N O2 SE) FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 MPD 3(C6 H14 O2) FORMUL 8 HOH *402(H2 O) HELIX 1 1 SER A 10 SER A 23 1 14 HELIX 2 2 LYS A 27 GLY A 31 5 5 HELIX 3 3 PRO A 43 LEU A 53 1 11 HELIX 4 4 ASP A 59 LEU A 62 5 4 HELIX 5 5 PHE A 63 LEU A 81 1 19 HELIX 6 6 GLY A 93 LYS A 115 1 23 HELIX 7 7 PHE A 133 ASP A 143 1 11 HELIX 8 8 ASP A 158 TYR A 169 1 12 HELIX 9 9 ASN A 188 ASN A 200 1 13 HELIX 10 10 PHE A 209 LEU A 217 5 9 HELIX 11 11 ASP A 218 LYS A 222 5 5 HELIX 12 12 ASP A 231 GLY A 235 5 5 HELIX 13 13 ASP A 260 LEU A 267 5 8 HELIX 14 14 GLY A 288 ASN A 327 1 40 HELIX 15 15 ASP A 346 ARG A 357 1 12 HELIX 16 16 LYS A 379 LYS A 394 1 16 HELIX 17 17 SER B 10 SER B 23 1 14 HELIX 18 18 LYS B 27 GLY B 31 5 5 HELIX 19 19 PRO B 43 LEU B 53 1 11 HELIX 20 20 ASP B 59 LEU B 62 5 4 HELIX 21 21 PHE B 63 LEU B 81 1 19 HELIX 22 22 GLY B 93 LYS B 115 1 23 HELIX 23 23 PHE B 133 ASP B 143 1 11 HELIX 24 24 ASP B 158 TYR B 169 1 12 HELIX 25 25 ASN B 188 ASN B 200 1 13 HELIX 26 26 PHE B 209 LEU B 217 5 9 HELIX 27 27 ASP B 218 LYS B 222 5 5 HELIX 28 28 ASP B 231 GLY B 235 5 5 HELIX 29 29 ASP B 260 LEU B 267 5 8 HELIX 30 30 GLY B 288 ASN B 327 1 40 HELIX 31 31 ASP B 346 ARG B 357 1 12 HELIX 32 32 LYS B 379 LYS B 394 1 16 SHEET 1 A 7 TYR A 87 VAL A 91 0 SHEET 2 A 7 GLY A 254 PHE A 258 -1 O PHE A 258 N TYR A 87 SHEET 3 A 7 SER A 238 THR A 240 -1 N ILE A 239 O LEU A 257 SHEET 4 A 7 TYR A 202 ASP A 206 1 N VAL A 205 O THR A 240 SHEET 5 A 7 GLY A 173 ILE A 177 1 N GLY A 176 O ASP A 206 SHEET 6 A 7 LYS A 124 PRO A 128 1 N ILE A 126 O GLY A 173 SHEET 7 A 7 GLU A 145 ALA A 149 1 O ILE A 147 N ILE A 125 SHEET 1 B 2 VAL A 269 ASP A 270 0 SHEET 2 B 2 ARG A 278 GLN A 279 -1 O GLN A 279 N VAL A 269 SHEET 1 C 3 ILE A 339 GLU A 343 0 SHEET 2 C 3 ALA A 369 VAL A 373 -1 O ILE A 372 N VAL A 340 SHEET 3 C 3 SER A 362 VAL A 363 -1 N SER A 362 O ARG A 371 SHEET 1 D 7 TYR B 87 VAL B 91 0 SHEET 2 D 7 GLY B 254 PHE B 258 -1 O PHE B 258 N TYR B 87 SHEET 3 D 7 SER B 238 THR B 240 -1 N ILE B 239 O LEU B 257 SHEET 4 D 7 TYR B 202 ASP B 206 1 N VAL B 205 O SER B 238 SHEET 5 D 7 GLY B 173 ILE B 177 1 N GLY B 176 O ASP B 206 SHEET 6 D 7 LYS B 124 PRO B 128 1 N ILE B 126 O GLY B 173 SHEET 7 D 7 GLU B 145 ALA B 149 1 O ALA B 149 N VAL B 127 SHEET 1 E 2 VAL B 269 ASP B 270 0 SHEET 2 E 2 ARG B 278 GLN B 279 -1 O GLN B 279 N VAL B 269 SHEET 1 F 3 ILE B 339 GLU B 343 0 SHEET 2 F 3 ALA B 369 VAL B 373 -1 O ILE B 372 N VAL B 340 SHEET 3 F 3 SER B 362 VAL B 363 -1 N SER B 362 O ARG B 371 LINK C MSE A 1 N ARG A 2 1555 1555 1.34 LINK C ASN A 3 N MSE A 4 1555 1555 1.33 LINK C MSE A 4 N GLN A 5 1555 1555 1.32 LINK C SER A 36 N MSE A 37 1555 1555 1.33 LINK C MSE A 37 N CYS A 38 1555 1555 1.33 LINK C LEU A 99 N MSE A 100 1555 1555 1.34 LINK C MSE A 100 N ALA A 101 1555 1555 1.33 LINK C GLU A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N MSE A 142 1555 1555 1.32 LINK C MSE A 142 N ASP A 143 1555 1555 1.33 LINK C LYS A 245 N MSE A 246 1555 1555 1.33 LINK C MSE A 246 N GLY A 247 1555 1555 1.33 LINK C CYS A 313 N MSE A 314 1555 1555 1.34 LINK C MSE A 314 N GLU A 315 1555 1555 1.33 LINK C VAL A 374 N MSE A 375 1555 1555 1.32 LINK C MSE A 375 N PRO A 376 1555 1555 1.35 LINK C ASN B 3 N MSE B 4 1555 1555 1.33 LINK C MSE B 4 N GLN B 5 1555 1555 1.33 LINK C SER B 36 N MSE B 37 1555 1555 1.33 LINK C MSE B 37 N CYS B 38 1555 1555 1.32 LINK C LEU B 99 N MSE B 100 1555 1555 1.32 LINK C MSE B 100 N ALA B 101 1555 1555 1.34 LINK C GLU B 140 N MSE B 141 1555 1555 1.33 LINK C MSE B 141 N MSE B 142 1555 1555 1.33 LINK C MSE B 142 N ASP B 143 1555 1555 1.34 LINK C LYS B 245 N MSE B 246 1555 1555 1.33 LINK C MSE B 246 N GLY B 247 1555 1555 1.33 LINK C CYS B 313 N MSE B 314 1555 1555 1.34 LINK C MSE B 314 N GLU B 315 1555 1555 1.33 LINK C VAL B 374 N MSE B 375 1555 1555 1.32 LINK C MSE B 375 N PRO B 376 1555 1555 1.35 CISPEP 1 ILE A 251 PRO A 252 0 -2.64 CISPEP 2 ILE B 251 PRO B 252 0 -3.21 SITE 1 AC1 16 MSE A 37 GLY A 93 GLY A 94 THR A 95 SITE 2 AC1 16 ASN A 98 HIS A 132 THR A 181 ASP A 206 SITE 3 AC1 16 ALA A 208 ASP A 242 HIS A 244 LYS A 245 SITE 4 AC1 16 HOH A 580 HOH A 587 HOH A 700 THR B 285 SITE 1 AC2 16 THR A 285 MSE B 37 GLY B 93 GLY B 94 SITE 2 AC2 16 THR B 95 ASN B 98 HIS B 132 THR B 181 SITE 3 AC2 16 ASP B 206 ALA B 208 ASP B 242 HIS B 244 SITE 4 AC2 16 LYS B 245 HOH B 482 HOH B 506 HOH B 719 SITE 1 AC3 5 PRO A 272 HOH A 512 ALA B 131 HIS B 132 SITE 2 AC3 5 HOH B 519 SITE 1 AC4 4 ILE A 129 ALA A 131 HOH A 539 HOH B 714 SITE 1 AC5 1 ASP A 50 CRYST1 85.276 104.128 119.915 90.00 90.00 90.00 P 21 21 21 8 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 0.011727 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009604 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008339 0.00000 HETATM 1 N MSE A 1 15.626 79.140 36.017 1.00 81.01 N HETATM 2 CA MSE A 1 15.199 80.195 36.987 1.00 82.89 C HETATM 3 C MSE A 1 16.211 81.278 37.360 1.00 75.06 C HETATM 4 O MSE A 1 17.412 81.152 37.104 1.00 75.48 O HETATM 5 CB MSE A 1 14.750 79.568 38.296 1.00 83.33 C HETATM 6 CG MSE A 1 13.283 79.219 38.354 1.00 88.35 C HETATM 7 SE MSE A 1 12.616 80.050 40.007 0.75 98.34 SE HETATM 8 CE MSE A 1 12.524 82.041 39.359 1.00 86.50 C