HEADER HYDROLASE 02-MAR-16 5IJG TITLE CRYSTAL STRUCTURE OF O-ACETYLHOMOSERINE SULFHYDROLASE FROM BRUCELLA TITLE 2 MELITENSIS AT 2.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYS/MET METABOLISM PYRIDOXAL-PHOSPHATE-DEPENDENT ENZYME; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYSTATHIONINE GAMMA-SYNTHASE; COMPND 5 EC: 2.5.1.48; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA MELITENSIS BIOTYPE 1 (STRAIN 16M / SOURCE 3 ATCC 23456 / NCTC 10094); SOURCE 4 ORGANISM_TAXID: 224914; SOURCE 5 GENE: BMEI0103, BAWG_0092; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS O-ACETYLHOMOSERINE, SULFHYDROLASE, BRUCELLA MELITENSIS, PLP, KEYWDS 2 PYRIDOXAL, TRANSFERASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.BOYKO,A.Y.NIKOLAEVA,V.V.KOOLIKOVA,M.I.KOTLOV,T.V.DEMIDKINA, AUTHOR 2 V.O.POPOV REVDAT 2 10-JAN-24 5IJG 1 REMARK REVDAT 1 05-APR-17 5IJG 0 JRNL AUTH K.M.BOYKO,A.Y.NIKOLAEVA,V.KOOLIKOVA,T.V.DEMIDKINA,V.O.POPOV JRNL TITL CRYSTAL STRUCTURE OF O-ACETYLHOMOSERINE SULFHYDROLASE FROM JRNL TITL 2 BRUCELLA MELITENSIS AT 2.0 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 95.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 49750 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2599 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3636 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5587 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 487 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.67000 REMARK 3 B22 (A**2) : 12.67000 REMARK 3 B33 (A**2) : -25.33000 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): 0.036 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.614 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5746 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5450 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7802 ; 1.951 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12491 ; 1.503 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 750 ; 6.825 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 235 ;36.156 ;23.787 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 874 ;16.278 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;19.827 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 915 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6548 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1282 ; 0.002 ; 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): 3018 ; 3.875 ; 4.024 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3017 ; 3.875 ; 4.023 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3762 ; 4.840 ; 6.015 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3763 ; 4.839 ; 6.016 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2728 ; 4.587 ; 4.381 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2728 ; 4.584 ; 4.381 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4041 ; 6.334 ; 6.432 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6641 ; 7.677 ;33.222 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6642 ; 7.678 ;33.225 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5IJG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-12 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.17 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52389 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 95.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.30 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 16.00 REMARK 200 R MERGE FOR SHELL (I) : 1.16400 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: BALBES REMARK 200 STARTING MODEL: 3NMY REMARK 200 REMARK 200 REMARK: ROD-LIKE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM DI-AMMONIUM TARTRATE PH 7.0, REMARK 280 12% PEG3350, 4 MM N-DECYL-B-D-MALTOPYRANOSIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 73.84667 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 36.92333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.92333 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 73.84667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -36.92333 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 SER A 7 REMARK 465 LYS A 8 REMARK 465 ILE A 9 REMARK 465 ARG A 10 REMARK 465 LEU A 11 REMARK 465 GLY A 12 REMARK 465 ASN A 13 REMARK 465 HIS A 14 REMARK 465 ASN A 24 REMARK 465 TYR A 25 REMARK 465 GLY A 26 REMARK 465 TYR A 27 REMARK 465 ASP A 28 REMARK 465 SER A 29 REMARK 465 GLU A 30 REMARK 465 LEU A 31 REMARK 465 SER A 32 REMARK 465 GLU A 33 REMARK 465 GLY A 34 REMARK 465 ALA A 35 REMARK 465 VAL A 36 REMARK 465 LYS A 37 REMARK 465 PRO A 38 REMARK 465 PRO A 39 REMARK 465 VAL A 40 REMARK 465 PHE A 41 REMARK 465 LEU A 42 REMARK 465 THR A 43 REMARK 465 SER A 44 REMARK 465 THR A 45 REMARK 465 PHE A 46 REMARK 465 VAL A 47 REMARK 465 PHE A 48 REMARK 465 LYS A 49 REMARK 465 THR A 50 REMARK 465 ALA A 51 REMARK 465 GLU A 52 REMARK 465 ASP A 53 REMARK 465 GLY A 54 REMARK 465 ARG A 55 REMARK 465 ASP A 56 REMARK 465 PHE A 57 REMARK 465 PHE A 58 REMARK 465 ASP A 59 REMARK 465 PHE A 60 REMARK 465 VAL A 61 REMARK 465 SER A 62 REMARK 465 GLY A 63 REMARK 465 ARG A 64 REMARK 465 LYS A 65 REMARK 465 GLU A 66 REMARK 465 PRO A 67 REMARK 465 PRO A 68 REMARK 465 ALA A 69 REMARK 465 GLY A 70 REMARK 465 VAL A 71 REMARK 465 GLY A 72 REMARK 465 ALA A 73 REMARK 465 GLY A 74 REMARK 465 LEU A 75 REMARK 465 VAL A 76 REMARK 465 TYR A 77 REMARK 465 SER A 78 REMARK 465 ARG A 79 REMARK 465 PHE A 80 REMARK 465 ASN A 81 REMARK 465 HIS A 82 REMARK 465 PRO A 83 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 3 REMARK 465 PRO B 4 REMARK 465 ARG B 5 REMARK 465 PRO B 6 REMARK 465 PRO B 68 REMARK 465 ALA B 69 REMARK 465 GLY B 70 REMARK 465 VAL B 71 REMARK 465 GLY B 72 REMARK 465 ALA B 73 REMARK 465 GLY B 74 REMARK 465 SER B 370 REMARK 465 LEU B 371 REMARK 465 GLY B 372 REMARK 465 MET B 384 REMARK 465 THR B 385 REMARK 465 HIS B 386 REMARK 465 SER B 387 REMARK 465 GLY B 388 REMARK 465 VAL B 389 REMARK 465 PRO B 390 REMARK 465 ALA B 427 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 LEU A 15 CG CD1 CD2 REMARK 470 ARG A 91 CZ NH1 NH2 REMARK 470 LYS A 141 CE NZ REMARK 470 LYS A 164 CG CD CE NZ REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 258 CG CD CE NZ REMARK 470 ARG A 262 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 285 CD NE CZ NH1 NH2 REMARK 470 GLU A 325 CG CD OE1 OE2 REMARK 470 LYS A 334 CG CD CE NZ REMARK 470 LYS B 8 CG CD CE NZ REMARK 470 ILE B 9 CG1 CG2 CD1 REMARK 470 ARG B 10 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 33 CG CD OE1 OE2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 LYS B 65 CD CE NZ REMARK 470 LEU B 75 CG CD1 CD2 REMARK 470 GLU B 86 CD OE1 OE2 REMARK 470 LYS B 164 CG CD CE NZ REMARK 470 LYS B 172 CE NZ REMARK 470 ARG B 206 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 246 CG ND1 CD2 CE1 NE2 REMARK 470 SER B 247 OG REMARK 470 LYS B 316 CG CD CE NZ REMARK 470 ASP B 324 CG OD1 OD2 REMARK 470 GLU B 325 CG CD OE1 OE2 REMARK 470 ARG B 326 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 352 CD OE1 NE2 REMARK 470 LYS B 366 CG CD CE NZ REMARK 470 VAL B 369 CG1 CG2 REMARK 470 VAL B 391 CG1 CG2 REMARK 470 VAL B 393 CG1 CG2 REMARK 470 ARG B 394 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 396 CG CD NE CZ NH1 NH2 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 LEU A 126 CB - CG - CD2 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG B 55 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG B 120 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 174 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 210 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP B 276 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 296 CG - CD - NE ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG B 296 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 296 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 141 -74.84 -100.70 REMARK 500 TYR A 242 -41.96 -141.43 REMARK 500 MET A 384 -101.44 -117.88 REMARK 500 HIS B 82 65.74 -118.55 REMARK 500 LYS B 141 -75.18 -109.54 REMARK 500 ALA B 368 -146.95 -160.97 REMARK 500 THR B 374 -59.99 83.43 REMARK 500 GLU B 411 171.83 -54.13 REMARK 500 LEU B 424 59.53 -67.40 REMARK 500 ASP B 425 73.01 -33.19 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 TYR A 237 SER A 238 145.56 REMARK 500 TYR B 237 SER B 238 148.58 REMARK 500 LEU B 424 ASP B 425 -123.48 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 501 and LYS B REMARK 800 241 DBREF 5IJG A 1 427 UNP Q8YJI0 Q8YJI0_BRUME 1 427 DBREF 5IJG B 1 427 UNP Q8YJI0 Q8YJI0_BRUME 1 427 SEQRES 1 A 427 MET THR ALA PRO ARG PRO SER LYS ILE ARG LEU GLY ASN SEQRES 2 A 427 HIS LEU LEU HIS PRO GLU THR GLN MET LEU ASN TYR GLY SEQRES 3 A 427 TYR ASP SER GLU LEU SER GLU GLY ALA VAL LYS PRO PRO SEQRES 4 A 427 VAL PHE LEU THR SER THR PHE VAL PHE LYS THR ALA GLU SEQRES 5 A 427 ASP GLY ARG ASP PHE PHE ASP PHE VAL SER GLY ARG LYS SEQRES 6 A 427 GLU PRO PRO ALA GLY VAL GLY ALA GLY LEU VAL TYR SER SEQRES 7 A 427 ARG PHE ASN HIS PRO ASN SER GLU ILE VAL GLU ASP ARG SEQRES 8 A 427 LEU ALA VAL TYR GLU GLY ALA GLU SER ALA ALA LEU PHE SEQRES 9 A 427 SER SER GLY MET SER ALA ILE ALA THR THR LEU PHE ALA SEQRES 10 A 427 PHE VAL ARG PRO GLY ASP VAL ILE LEU HIS SER GLN PRO SEQRES 11 A 427 LEU TYR GLY GLY THR GLU THR LEU LEU ALA LYS THR PHE SEQRES 12 A 427 PHE ASN PHE GLY VAL GLU ALA VAL ALA PHE ALA ASP GLY SEQRES 13 A 427 VAL HIS GLU ALA THR ILE GLU LYS ALA ALA GLU GLU ALA SEQRES 14 A 427 LEU ALA LYS GLY ARG VAL SER VAL ILE LEU ILE GLU THR SEQRES 15 A 427 PRO ALA ASN PRO THR ASN SER ILE VAL ASP VAL ALA ALA SEQRES 16 A 427 VAL ARG ARG VAL ALA GLU LYS ILE GLU ALA ARG GLN GLY SEQRES 17 A 427 SER ARG PRO VAL ILE ALA CYS ASP ASN THR LEU LEU GLY SEQRES 18 A 427 PRO VAL PHE GLN LYS PRO LEU ASP HIS GLY ALA ASP LEU SEQRES 19 A 427 SER VAL TYR SER LEU THR LYS TYR VAL GLY GLY HIS SER SEQRES 20 A 427 ASP LEU ILE ALA GLY ALA VAL LEU GLY ALA LYS SER VAL SEQRES 21 A 427 VAL ARG GLN VAL LYS ALA LEU ARG GLY ALA ILE GLY THR SEQRES 22 A 427 GLN LEU ASP PRO HIS SER CYS TRP MET LEU GLY ARG SER SEQRES 23 A 427 LEU GLU THR LEU GLY LEU ARG MET GLU ARG ALA ASP SER SEQRES 24 A 427 ASN ALA ARG ALA ILE ALA GLU PHE LEU ARG ASN HIS PRO SEQRES 25 A 427 LYS VAL GLU LYS LEU HIS TYR LEU PRO PHE ALA ASP GLU SEQRES 26 A 427 ARG SER ASP ILE ALA ALA LEU PHE LYS ARG GLN CYS THR SEQRES 27 A 427 GLY ALA GLY SER THR PHE SER PHE ASP ILE LYS GLY GLY SEQRES 28 A 427 GLN ALA ALA ALA PHE ARG PHE LEU ASN ALA LEU GLN ILE SEQRES 29 A 427 LEU LYS LEU ALA VAL SER LEU GLY GLY THR GLU SER LEU SEQRES 30 A 427 ALA SER HIS PRO ALA ALA MET THR HIS SER GLY VAL PRO SEQRES 31 A 427 VAL ASP VAL ARG GLU ARG ILE GLY VAL LEU GLU SER THR SEQRES 32 A 427 ILE ARG LEU SER ILE GLY ILE GLU HIS PRO ASP ASP LEU SEQRES 33 A 427 ILE ALA ASP LEU ALA GLN ALA LEU ASP ALA ALA SEQRES 1 B 427 MET THR ALA PRO ARG PRO SER LYS ILE ARG LEU GLY ASN SEQRES 2 B 427 HIS LEU LEU HIS PRO GLU THR GLN MET LEU ASN TYR GLY SEQRES 3 B 427 TYR ASP SER GLU LEU SER GLU GLY ALA VAL LYS PRO PRO SEQRES 4 B 427 VAL PHE LEU THR SER THR PHE VAL PHE LYS THR ALA GLU SEQRES 5 B 427 ASP GLY ARG ASP PHE PHE ASP PHE VAL SER GLY ARG LYS SEQRES 6 B 427 GLU PRO PRO ALA GLY VAL GLY ALA GLY LEU VAL TYR SER SEQRES 7 B 427 ARG PHE ASN HIS PRO ASN SER GLU ILE VAL GLU ASP ARG SEQRES 8 B 427 LEU ALA VAL TYR GLU GLY ALA GLU SER ALA ALA LEU PHE SEQRES 9 B 427 SER SER GLY MET SER ALA ILE ALA THR THR LEU PHE ALA SEQRES 10 B 427 PHE VAL ARG PRO GLY ASP VAL ILE LEU HIS SER GLN PRO SEQRES 11 B 427 LEU TYR GLY GLY THR GLU THR LEU LEU ALA LYS THR PHE SEQRES 12 B 427 PHE ASN PHE GLY VAL GLU ALA VAL ALA PHE ALA ASP GLY SEQRES 13 B 427 VAL HIS GLU ALA THR ILE GLU LYS ALA ALA GLU GLU ALA SEQRES 14 B 427 LEU ALA LYS GLY ARG VAL SER VAL ILE LEU ILE GLU THR SEQRES 15 B 427 PRO ALA ASN PRO THR ASN SER ILE VAL ASP VAL ALA ALA SEQRES 16 B 427 VAL ARG ARG VAL ALA GLU LYS ILE GLU ALA ARG GLN GLY SEQRES 17 B 427 SER ARG PRO VAL ILE ALA CYS ASP ASN THR LEU LEU GLY SEQRES 18 B 427 PRO VAL PHE GLN LYS PRO LEU ASP HIS GLY ALA ASP LEU SEQRES 19 B 427 SER VAL TYR SER LEU THR LYS TYR VAL GLY GLY HIS SER SEQRES 20 B 427 ASP LEU ILE ALA GLY ALA VAL LEU GLY ALA LYS SER VAL SEQRES 21 B 427 VAL ARG GLN VAL LYS ALA LEU ARG GLY ALA ILE GLY THR SEQRES 22 B 427 GLN LEU ASP PRO HIS SER CYS TRP MET LEU GLY ARG SER SEQRES 23 B 427 LEU GLU THR LEU GLY LEU ARG MET GLU ARG ALA ASP SER SEQRES 24 B 427 ASN ALA ARG ALA ILE ALA GLU PHE LEU ARG ASN HIS PRO SEQRES 25 B 427 LYS VAL GLU LYS LEU HIS TYR LEU PRO PHE ALA ASP GLU SEQRES 26 B 427 ARG SER ASP ILE ALA ALA LEU PHE LYS ARG GLN CYS THR SEQRES 27 B 427 GLY ALA GLY SER THR PHE SER PHE ASP ILE LYS GLY GLY SEQRES 28 B 427 GLN ALA ALA ALA PHE ARG PHE LEU ASN ALA LEU GLN ILE SEQRES 29 B 427 LEU LYS LEU ALA VAL SER LEU GLY GLY THR GLU SER LEU SEQRES 30 B 427 ALA SER HIS PRO ALA ALA MET THR HIS SER GLY VAL PRO SEQRES 31 B 427 VAL ASP VAL ARG GLU ARG ILE GLY VAL LEU GLU SER THR SEQRES 32 B 427 ILE ARG LEU SER ILE GLY ILE GLU HIS PRO ASP ASP LEU SEQRES 33 B 427 ILE ALA ASP LEU ALA GLN ALA LEU ASP ALA ALA HET PLP A 501 15 HET PLP B 501 15 HET GOL B 502 6 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM GOL GLYCEROL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *487(H2 O) HELIX 1 AA1 HIS A 17 MET A 22 1 6 HELIX 2 AA2 SER A 85 GLY A 97 1 13 HELIX 3 AA3 SER A 106 VAL A 119 1 14 HELIX 4 AA4 TYR A 132 LYS A 141 1 10 HELIX 5 AA5 LYS A 141 PHE A 146 1 6 HELIX 6 AA6 HIS A 158 ALA A 171 1 14 HELIX 7 AA7 ASP A 192 GLY A 208 1 17 HELIX 8 AA8 LYS A 226 HIS A 230 5 5 HELIX 9 AA9 ALA A 257 GLY A 272 1 16 HELIX 10 AB1 ASP A 276 GLU A 288 1 13 HELIX 11 AB2 THR A 289 ASN A 310 1 22 HELIX 12 AB3 TYR A 319 ALA A 323 5 5 HELIX 13 AB4 SER A 327 CYS A 337 1 11 HELIX 14 AB5 GLY A 350 LEU A 362 1 13 HELIX 15 AB6 PRO A 390 ILE A 397 1 8 HELIX 16 AB7 HIS A 412 ALA A 427 1 16 HELIX 17 AB8 HIS B 17 TYR B 25 1 9 HELIX 18 AB9 TYR B 27 SER B 29 5 3 HELIX 19 AC1 THR B 50 SER B 62 1 13 HELIX 20 AC2 ASN B 84 GLY B 97 1 14 HELIX 21 AC3 SER B 106 VAL B 119 1 14 HELIX 22 AC4 TYR B 132 LYS B 141 1 10 HELIX 23 AC5 PHE B 143 GLY B 147 5 5 HELIX 24 AC6 HIS B 158 GLY B 173 1 16 HELIX 25 AC7 ASP B 192 GLY B 208 1 17 HELIX 26 AC8 LYS B 226 GLY B 231 5 6 HELIX 27 AC9 ALA B 257 GLY B 272 1 16 HELIX 28 AD1 ASP B 276 ARG B 309 1 34 HELIX 29 AD2 TYR B 319 ALA B 323 5 5 HELIX 30 AD3 SER B 327 CYS B 337 1 11 HELIX 31 AD4 GLY B 350 LEU B 362 1 13 HELIX 32 AD5 ASP B 392 GLY B 398 1 7 HELIX 33 AD6 HIS B 412 LEU B 424 1 13 SHEET 1 AA1 7 SER A 100 PHE A 104 0 SHEET 2 AA1 7 GLY A 252 GLY A 256 -1 O VAL A 254 N ALA A 102 SHEET 3 AA1 7 LEU A 234 SER A 238 -1 N SER A 235 O LEU A 255 SHEET 4 AA1 7 VAL A 212 ASP A 216 1 N CYS A 215 O VAL A 236 SHEET 5 AA1 7 ARG A 174 GLU A 181 1 N ILE A 180 O ASP A 216 SHEET 6 AA1 7 ASP A 123 HIS A 127 1 N LEU A 126 O LEU A 179 SHEET 7 AA1 7 GLU A 149 ALA A 152 1 O VAL A 151 N HIS A 127 SHEET 1 AA2 5 VAL A 314 HIS A 318 0 SHEET 2 AA2 5 THR A 343 ILE A 348 -1 O ASP A 347 N LYS A 316 SHEET 3 AA2 5 THR A 403 SER A 407 -1 O LEU A 406 N PHE A 344 SHEET 4 AA2 5 LEU A 377 SER A 379 -1 N SER A 379 O ARG A 405 SHEET 5 AA2 5 LYS A 366 LEU A 367 1 N LYS A 366 O ALA A 378 SHEET 1 AA3 2 ARG B 10 LEU B 11 0 SHEET 2 AA3 2 HIS B 14 LEU B 15 -1 O HIS B 14 N LEU B 11 SHEET 1 AA4 3 LEU B 31 GLY B 34 0 SHEET 2 AA4 3 VAL B 76 ARG B 79 -1 O SER B 78 N SER B 32 SHEET 3 AA4 3 PHE B 46 VAL B 47 -1 N VAL B 47 O TYR B 77 SHEET 1 AA5 7 SER B 100 PHE B 104 0 SHEET 2 AA5 7 GLY B 252 GLY B 256 -1 O GLY B 252 N PHE B 104 SHEET 3 AA5 7 LEU B 234 SER B 238 -1 N SER B 235 O LEU B 255 SHEET 4 AA5 7 VAL B 212 ASP B 216 1 N CYS B 215 O LEU B 234 SHEET 5 AA5 7 VAL B 175 GLU B 181 1 N ILE B 180 O ASP B 216 SHEET 6 AA5 7 VAL B 124 SER B 128 1 N LEU B 126 O LEU B 179 SHEET 7 AA5 7 GLU B 149 PHE B 153 1 O VAL B 151 N HIS B 127 SHEET 1 AA6 5 VAL B 314 HIS B 318 0 SHEET 2 AA6 5 THR B 343 ILE B 348 -1 O SER B 345 N HIS B 318 SHEET 3 AA6 5 THR B 403 SER B 407 -1 O ILE B 404 N PHE B 346 SHEET 4 AA6 5 LEU B 377 SER B 379 -1 N SER B 379 O ARG B 405 SHEET 5 AA6 5 LYS B 366 LEU B 367 1 N LYS B 366 O ALA B 378 LINK NZ LYS A 241 C4A PLP A 501 1555 1555 1.44 LINK NZ LYS B 241 C4A PLP B 501 1555 1555 1.45 CISPEP 1 GLN A 129 PRO A 130 0 -5.41 CISPEP 2 THR A 182 PRO A 183 0 -13.19 CISPEP 3 ASN A 185 PRO A 186 0 9.36 CISPEP 4 GLY A 221 PRO A 222 0 1.35 CISPEP 5 PRO B 38 PRO B 39 0 -2.96 CISPEP 6 GLN B 129 PRO B 130 0 -9.72 CISPEP 7 THR B 182 PRO B 183 0 -7.55 CISPEP 8 ASN B 185 PRO B 186 0 -17.78 CISPEP 9 GLY B 221 PRO B 222 0 4.74 SITE 1 AC1 13 SER A 106 GLY A 107 MET A 108 TYR A 132 SITE 2 AC1 13 GLU A 181 ASP A 216 SER A 238 THR A 240 SITE 3 AC1 13 LYS A 241 HOH A 607 HOH A 628 HOH A 629 SITE 4 AC1 13 HOH A 643 SITE 1 AC2 8 ARG A 357 GLN B 225 LYS B 226 ASP B 229 SITE 2 AC2 8 HIS B 230 GLN B 336 HOH B 606 HOH B 693 SITE 1 AC3 15 SER B 106 GLY B 107 MET B 108 TYR B 132 SITE 2 AC3 15 GLU B 181 ASP B 216 SER B 238 LEU B 239 SITE 3 AC3 15 THR B 240 TYR B 242 GLY B 373 HOH B 620 SITE 4 AC3 15 HOH B 630 HOH B 697 HOH B 711 CRYST1 109.710 109.710 110.770 90.00 90.00 120.00 P 32 2 1 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 0.009115 0.005263 0.000000 0.00000 SCALE2 0.000000 0.010525 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009028 0.00000