HEADER LYASE 12-JAN-18 6C4P TITLE CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE FROM SACCHAROMYCES TITLE 2 CEREVISIAE: THE STRUCTURE OF THE PMP COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATHIONINE BETA-SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BETA-THIONASE,SERINE SULFHYDRASE,SULFUR TRANSFER PROTEIN 4; COMPND 5 EC: 4.2.1.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: CYS4, STR4, YGR155W, G6667; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS CBS, SYNTHASE, PLP, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.KREINBRING,Y.TU,D.LIU,D.B.BERKOWITZ,G.A.PETSKO,D.RINGE REVDAT 5 04-OCT-23 6C4P 1 LINK REVDAT 4 01-JAN-20 6C4P 1 REMARK REVDAT 3 20-FEB-19 6C4P 1 REMARK REVDAT 2 20-JUN-18 6C4P 1 JRNL REVDAT 1 25-APR-18 6C4P 0 JRNL AUTH Y.TU,C.A.KREINBRING,M.HILL,C.LIU,G.A.PETSKO,C.D.MCCUNE, JRNL AUTH 2 D.B.BERKOWITZ,D.LIU,D.RINGE JRNL TITL CRYSTAL STRUCTURES OF CYSTATHIONINE BETA-SYNTHASE FROM JRNL TITL 2 SACCHAROMYCES CEREVISIAE: ONE ENZYMATIC STEP AT A TIME. JRNL REF BIOCHEMISTRY V. 57 3134 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29630349 JRNL DOI 10.1021/ACS.BIOCHEM.8B00092 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0173 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 16003 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1778 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1187 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 132 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2668 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 86 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.09000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -3.53000 REMARK 3 B12 (A**2) : 0.54000 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): 0.316 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.083 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2781 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2640 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3762 ; 1.521 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6148 ; 0.985 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 349 ; 6.507 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;37.200 ;25.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 487 ;13.886 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;17.461 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 421 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3068 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 512 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 5 A 348 REMARK 3 ORIGIN FOR THE GROUP (A): 1.2390 30.5730 -12.6630 REMARK 3 T TENSOR REMARK 3 T11: 0.1388 T22: 0.0432 REMARK 3 T33: 0.0416 T12: 0.0627 REMARK 3 T13: -0.0567 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 1.1456 L22: 0.9897 REMARK 3 L33: 2.5884 L12: -0.0627 REMARK 3 L13: 0.3172 L23: 0.5603 REMARK 3 S TENSOR REMARK 3 S11: 0.0950 S12: -0.0101 S13: -0.0988 REMARK 3 S21: 0.1063 S22: 0.1018 S23: -0.1486 REMARK 3 S31: 0.4899 S32: 0.2694 S33: -0.1969 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PHENIX, PDB-REDO, REFMAC REMARK 4 REMARK 4 6C4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231983. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.19500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 1JBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS, PH 8.0, 30% PEG400, 100 REMARK 280 MM CALCIUM ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 138.61533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 69.30767 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.96150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.65383 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 173.26917 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 138.61533 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 69.30767 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.65383 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 103.96150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 173.26917 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: 8090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL 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 BIOMT1 2 0.500000 0.866025 0.000000 -40.36650 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 69.91683 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -34.65383 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 686 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 ASP A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 LYS A 3 REMARK 465 SER A 4 REMARK 465 ASP A 349 REMARK 465 SER A 350 REMARK 465 SER A 351 REMARK 465 LYS A 352 REMARK 465 LEU A 353 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 O1 EDO A 509 O1 EDO A 509 12564 2.14 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 156 75.67 78.10 REMARK 500 LYS A 327 -109.89 -113.94 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 NA A 503 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 120 O REMARK 620 2 HOH A 606 O 78.3 REMARK 620 3 HOH A 634 O 84.0 153.9 REMARK 620 4 HOH A 637 O 70.7 68.1 88.1 REMARK 620 5 HOH A 651 O 79.8 104.4 91.0 150.4 REMARK 620 6 HOH A 679 O 167.1 93.8 106.7 116.0 92.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 183 O REMARK 620 2 ASP A 186 OD1 74.0 REMARK 620 3 ASP A 186 OD2 122.9 49.2 REMARK 620 4 ASN A 187 OD1 93.4 75.3 78.2 REMARK 620 5 GLN A 253 OE1 68.6 34.1 66.4 44.8 REMARK 620 6 HOH A 647 O 75.8 87.4 95.2 161.7 117.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PMP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6C2H RELATED DB: PDB REMARK 900 PLP INTERNAL ALDIMINE REMARK 900 RELATED ID: 6C2Q RELATED DB: PDB REMARK 900 PLP-L-SER REMARK 900 RELATED ID: 6C2Z RELATED DB: PDB REMARK 900 PLP-AMINOACRYLATE DBREF 6C4P A 1 353 UNP P32582 CBS_YEAST 1 353 SEQADV 6C4P MET A -21 UNP P32582 EXPRESSION TAG SEQADV 6C4P GLY A -20 UNP P32582 EXPRESSION TAG SEQADV 6C4P SER A -19 UNP P32582 EXPRESSION TAG SEQADV 6C4P SER A -18 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -17 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -16 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -15 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -14 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -13 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -12 UNP P32582 EXPRESSION TAG SEQADV 6C4P SER A -11 UNP P32582 EXPRESSION TAG SEQADV 6C4P SER A -10 UNP P32582 EXPRESSION TAG SEQADV 6C4P GLY A -9 UNP P32582 EXPRESSION TAG SEQADV 6C4P ASP A -8 UNP P32582 EXPRESSION TAG SEQADV 6C4P LEU A -7 UNP P32582 EXPRESSION TAG SEQADV 6C4P VAL A -6 UNP P32582 EXPRESSION TAG SEQADV 6C4P PRO A -5 UNP P32582 EXPRESSION TAG SEQADV 6C4P ARG A -4 UNP P32582 EXPRESSION TAG SEQADV 6C4P GLY A -3 UNP P32582 EXPRESSION TAG SEQADV 6C4P SER A -2 UNP P32582 EXPRESSION TAG SEQADV 6C4P HIS A -1 UNP P32582 EXPRESSION TAG SEQADV 6C4P MET A 0 UNP P32582 EXPRESSION TAG SEQRES 1 A 375 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 375 ASP LEU VAL PRO ARG GLY SER HIS MET MET THR LYS SER SEQRES 3 A 375 GLU GLN GLN ALA ASP SER ARG HIS ASN VAL ILE ASP LEU SEQRES 4 A 375 VAL GLY ASN THR PRO LEU ILE ALA LEU LYS LYS LEU PRO SEQRES 5 A 375 LYS ALA LEU GLY ILE LYS PRO GLN ILE TYR ALA LYS LEU SEQRES 6 A 375 GLU LEU TYR ASN PRO GLY GLY SER ILE LYS ASP ARG ILE SEQRES 7 A 375 ALA LYS SER MET VAL GLU GLU ALA GLU ALA SER GLY ARG SEQRES 8 A 375 ILE HIS PRO SER ARG SER THR LEU ILE GLU PRO THR SER SEQRES 9 A 375 GLY ASN THR GLY ILE GLY LEU ALA LEU ILE GLY ALA ILE SEQRES 10 A 375 LYS GLY TYR ARG THR ILE ILE THR LEU PRO GLU LYS MET SEQRES 11 A 375 SER ASN GLU LYS VAL SER VAL LEU LYS ALA LEU GLY ALA SEQRES 12 A 375 GLU ILE ILE ARG THR PRO THR ALA ALA ALA TRP ASP SER SEQRES 13 A 375 PRO GLU SER HIS ILE GLY VAL ALA LYS LYS LEU GLU LYS SEQRES 14 A 375 GLU ILE PRO GLY ALA VAL ILE LEU ASP GLN TYR ASN ASN SEQRES 15 A 375 MET MET ASN PRO GLU ALA HIS TYR PHE GLY THR GLY ARG SEQRES 16 A 375 GLU ILE GLN ARG GLN LEU GLU ASP LEU ASN LEU PHE ASP SEQRES 17 A 375 ASN LEU ARG ALA VAL VAL ALA GLY ALA GLY THR GLY GLY SEQRES 18 A 375 THR ILE SER GLY ILE SER LYS TYR LEU LYS GLU GLN ASN SEQRES 19 A 375 ASP LYS ILE GLN ILE VAL GLY ALA ASP PRO PHE GLY SER SEQRES 20 A 375 ILE LEU ALA GLN PRO GLU ASN LEU ASN LYS THR ASP ILE SEQRES 21 A 375 THR ASP TYR LYS VAL GLU GLY ILE GLY TYR ASP PHE VAL SEQRES 22 A 375 PRO GLN VAL LEU ASP ARG LYS LEU ILE ASP VAL TRP TYR SEQRES 23 A 375 LYS THR ASP ASP LYS PRO SER PHE LYS TYR ALA ARG GLN SEQRES 24 A 375 LEU ILE SER ASN GLU GLY VAL LEU VAL GLY GLY SER SER SEQRES 25 A 375 GLY SER ALA PHE THR ALA VAL VAL LYS TYR CYS GLU ASP SEQRES 26 A 375 HIS PRO GLU LEU THR GLU ASP ASP VAL ILE VAL ALA ILE SEQRES 27 A 375 PHE PRO ASP SER ILE ARG SER TYR LEU THR LYS PHE VAL SEQRES 28 A 375 ASP ASP GLU TRP LEU LYS LYS ASN ASN LEU TRP ASP ASP SEQRES 29 A 375 ASP VAL LEU ALA ARG PHE ASP SER SER LYS LEU HET PMP A 501 16 HET CA A 502 1 HET NA A 503 1 HET CL A 504 1 HET PEG A 505 7 HET PEG A 506 7 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 509 4 HETNAM PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETSYN PMP PYRIDOXAMINE-5'-PHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PMP C8 H13 N2 O5 P FORMUL 3 CA CA 2+ FORMUL 4 NA NA 1+ FORMUL 5 CL CL 1- FORMUL 6 PEG 2(C4 H10 O3) FORMUL 8 EDO 3(C2 H6 O2) FORMUL 11 HOH *86(H2 O) HELIX 1 AA1 VAL A 14 VAL A 18 5 5 HELIX 2 AA2 LYS A 28 LEU A 33 1 6 HELIX 3 AA3 LEU A 45 ASN A 47 5 3 HELIX 4 AA4 LYS A 53 SER A 67 1 15 HELIX 5 AA5 GLY A 83 GLY A 97 1 15 HELIX 6 AA6 SER A 109 LEU A 119 1 11 HELIX 7 AA7 SER A 137 LYS A 147 1 11 HELIX 8 AA8 MET A 161 GLY A 170 1 10 HELIX 9 AA9 GLY A 170 LEU A 182 1 13 HELIX 10 AB1 GLY A 198 ASN A 212 1 15 HELIX 11 AB2 PRO A 230 LYS A 235 5 6 HELIX 12 AB3 ASP A 256 ILE A 260 5 5 HELIX 13 AB4 ASP A 267 GLY A 283 1 17 HELIX 14 AB5 GLY A 287 HIS A 304 1 18 HELIX 15 AB6 SER A 320 LEU A 325 5 6 HELIX 16 AB7 ASP A 330 ASN A 337 1 8 HELIX 17 AB8 ASP A 341 ALA A 346 5 6 SHEET 1 AA1 6 LEU A 23 LEU A 26 0 SHEET 2 AA1 6 GLN A 38 LEU A 43 -1 O ALA A 41 N ILE A 24 SHEET 3 AA1 6 VAL A 312 PHE A 317 1 O ALA A 315 N LYS A 42 SHEET 4 AA1 6 LEU A 188 GLY A 194 1 N ARG A 189 O VAL A 312 SHEET 5 AA1 6 GLN A 216 PRO A 222 1 O VAL A 218 N VAL A 191 SHEET 6 AA1 6 VAL A 262 THR A 266 1 O TYR A 264 N GLY A 219 SHEET 1 AA2 4 GLU A 122 THR A 126 0 SHEET 2 AA2 4 ARG A 99 PRO A 105 1 N ILE A 102 O GLU A 122 SHEET 3 AA2 4 THR A 76 PRO A 80 1 N LEU A 77 O ARG A 99 SHEET 4 AA2 4 ALA A 152 VAL A 153 1 O VAL A 153 N THR A 76 LINK O GLY A 120 NA NA A 503 1555 1555 2.45 LINK O ASN A 183 CA CA A 502 1555 1555 2.41 LINK OD1 ASP A 186 CA CA A 502 1555 1555 2.35 LINK OD2 ASP A 186 CA CA A 502 1555 1555 2.74 LINK OD1 ASN A 187 CA CA A 502 1555 1555 2.37 LINK OE1 GLN A 253 CA CA A 502 1555 5555 2.52 LINK CA CA A 502 O HOH A 647 1555 1555 2.13 LINK NA NA A 503 O HOH A 606 1555 12564 2.48 LINK NA NA A 503 O HOH A 634 1555 1555 2.21 LINK NA NA A 503 O HOH A 637 1555 1555 2.24 LINK NA NA A 503 O HOH A 651 1555 1555 2.76 LINK NA NA A 503 O HOH A 679 1555 1555 2.39 CISPEP 1 GLN A 229 PRO A 230 0 -3.15 SITE 1 AC1 19 LYS A 53 SER A 82 ASN A 84 ALA A 195 SITE 2 AC1 19 GLY A 196 THR A 197 GLY A 198 GLY A 199 SITE 3 AC1 19 THR A 200 GLY A 245 ILE A 246 SER A 289 SITE 4 AC1 19 PRO A 318 ASP A 319 HOH A 601 HOH A 603 SITE 5 AC1 19 HOH A 621 HOH A 645 HOH A 659 SITE 1 AC2 5 ASN A 183 ASP A 186 ASN A 187 GLN A 253 SITE 2 AC2 5 HOH A 647 SITE 1 AC3 6 GLY A 120 HOH A 606 HOH A 634 HOH A 637 SITE 2 AC3 6 HOH A 651 HOH A 679 SITE 1 AC4 3 LYS A 107 MET A 108 GLY A 245 SITE 1 AC5 2 GLU A 136 ALA A 166 SITE 1 AC6 2 GLU A 165 TYR A 168 SITE 1 AC7 1 GLU A 122 SITE 1 AC8 7 PRO A 222 PHE A 223 TYR A 241 THR A 266 SITE 2 AC8 7 ASP A 267 ASP A 268 HOH A 638 SITE 1 AC9 4 LEU A 45 ASN A 47 PRO A 48 HOH A 653 CRYST1 80.733 80.733 207.923 90.00 90.00 120.00 P 65 2 2 12 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 0.012387 0.007151 0.000000 0.00000 SCALE2 0.000000 0.014303 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004809 0.00000