HEADER LYASE 11-AUG-15 5D5S TITLE CRYSTAL STRUCTURE OF METHIONINE GAMMA-LYASE FROM CITROBACTER FREUNDII, TITLE 2 S339A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE GAMMA-LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.4.1.11; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: S339A SUBSTITUTION AND SOME CYS WERE OXIDIZED TO CSO SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER FREUNDII; SOURCE 3 ORGANISM_TAXID: 546; SOURCE 4 GENE: TN42_08855, TO64_18625; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS METHIONINE GAMMA-LYASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.REVTOVICH,A.D.NIKULIN,N.V.ANUFRIEVA,E.A.MOROZOVA,T.V.DEMIDKINA REVDAT 2 10-JAN-24 5D5S 1 LINK ATOM REVDAT 1 17-AUG-16 5D5S 0 JRNL AUTH S.V.REVTOVICH,A.D.NIKULIN,N.V.ANUFRIEVA,E.A.MOROZOVA, JRNL AUTH 2 T.V.DEMIDKINA JRNL TITL THE CRYSTAL STRUCTURE OF METHIONINE GAMMA-LYASE FROM JRNL TITL 2 CITROBACTER FREUNDII, S339A MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 49320 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 2503 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.0000 - 4.4498 0.98 2764 138 0.1628 0.1727 REMARK 3 2 4.4498 - 3.5341 0.99 2689 136 0.1454 0.1644 REMARK 3 3 3.5341 - 3.0880 0.99 2651 130 0.1600 0.1898 REMARK 3 4 3.0880 - 2.8059 0.99 2621 135 0.1723 0.2086 REMARK 3 5 2.8059 - 2.6050 0.99 2608 132 0.1718 0.2082 REMARK 3 6 2.6050 - 2.4515 0.99 2604 141 0.1750 0.2220 REMARK 3 7 2.4515 - 2.3288 0.99 2606 136 0.1734 0.2112 REMARK 3 8 2.3288 - 2.2274 0.99 2587 131 0.1792 0.2154 REMARK 3 9 2.2274 - 2.1417 0.99 2619 149 0.1852 0.2415 REMARK 3 10 2.1417 - 2.0678 1.00 2592 141 0.1837 0.1909 REMARK 3 11 2.0678 - 2.0032 1.00 2636 125 0.1832 0.2214 REMARK 3 12 2.0032 - 1.9460 1.00 2533 154 0.1928 0.2366 REMARK 3 13 1.9460 - 1.8947 1.00 2587 160 0.2058 0.2539 REMARK 3 14 1.8947 - 1.8485 1.00 2617 134 0.2182 0.2644 REMARK 3 15 1.8485 - 1.8065 0.98 2507 165 0.2077 0.2840 REMARK 3 16 1.8065 - 1.7681 0.98 2558 139 0.2220 0.2476 REMARK 3 17 1.7681 - 1.7327 0.97 2483 131 0.2222 0.2651 REMARK 3 18 1.7327 - 1.7000 0.97 2555 126 0.2336 0.3140 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 2981 REMARK 3 ANGLE : 1.095 4052 REMARK 3 CHIRALITY : 0.047 469 REMARK 3 PLANARITY : 0.005 527 REMARK 3 DIHEDRAL : 15.912 1096 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5D5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212712. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49574 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2RFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG2000 MME, 50 MM TRIS-HCL, 0.2 MM REMARK 280 PLP, 0.25% DTT, PH 8.5,, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.32950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.54500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.39250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.32950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.54500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.39250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.32950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.54500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.39250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.32950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.54500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 64.39250 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: 22520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 47340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -142.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 516 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 702 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 729 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 827 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 1 REMARK 465 ALA A 46 REMARK 465 ALA A 47 REMARK 465 ARG A 48 REMARK 465 PHE A 49 REMARK 465 ALA A 50 REMARK 465 LEU A 51 REMARK 465 GLU A 52 REMARK 465 GLU A 53 REMARK 465 SER A 54 REMARK 465 GLY A 55 REMARK 465 TYR A 56 REMARK 465 ILE A 57 REMARK 465 TYR A 58 REMARK 465 THR A 59 REMARK 465 ARG A 60 REMARK 465 LEU A 61 REMARK 465 PHE A 398 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 692 O HOH A 806 1.41 REMARK 500 O HOH A 512 O HOH A 812 1.67 REMARK 500 OE1 GLU A 156 O HOH A 501 1.74 REMARK 500 O HOH A 597 O HOH A 699 1.79 REMARK 500 O HOH A 573 O HOH A 805 1.87 REMARK 500 O HOH A 715 O HOH A 740 1.88 REMARK 500 ND1 HIS A 117 O HOH A 502 1.90 REMARK 500 O HOH A 649 O HOH A 736 1.94 REMARK 500 O HOH A 737 O HOH A 790 1.95 REMARK 500 O HOH A 755 O HOH A 827 1.98 REMARK 500 O HOH A 610 O HOH A 847 2.00 REMARK 500 O HOH A 524 O HOH A 718 2.02 REMARK 500 O HOH A 550 O HOH A 715 2.10 REMARK 500 OE1 GLU A 322 O HOH A 503 2.10 REMARK 500 O HOH A 677 O HOH A 829 2.10 REMARK 500 O HOH A 803 O HOH A 858 2.11 REMARK 500 OE1 GLN A 102 O HOH A 504 2.11 REMARK 500 O HOH A 695 O HOH A 832 2.12 REMARK 500 O HOH A 791 O HOH A 881 2.12 REMARK 500 O HOH A 695 O HOH A 763 2.15 REMARK 500 O HOH A 714 O HOH A 875 2.16 REMARK 500 O HOH A 514 O HOH A 546 2.17 REMARK 500 O HOH A 793 O HOH A 877 2.17 REMARK 500 O HOH A 796 O HOH A 850 2.17 REMARK 500 O HOH A 814 O HOH A 852 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 646 O HOH A 674 2555 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 SER A 190 159.48 68.41 REMARK 500 LYS A 210 -119.87 -89.93 REMARK 500 ILE A 241 -64.53 -135.66 REMARK 500 MET A 353 -93.48 -93.75 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 365 ALA A 366 146.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 886 DISTANCE = 6.01 ANGSTROMS REMARK 525 HOH A 887 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH A 888 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH A 889 DISTANCE = 6.77 ANGSTROMS REMARK 525 HOH A 890 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A 891 DISTANCE = 7.62 ANGSTROMS REMARK 525 HOH A 892 DISTANCE = 8.20 ANGSTROMS REMARK 525 HOH A 893 DISTANCE = 9.31 ANGSTROMS 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 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 344 OE2 REMARK 620 2 HOH A 515 O 86.1 REMARK 620 3 HOH A 520 O 79.5 8.4 REMARK 620 4 HOH A 620 O 87.3 8.2 8.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RFV RELATED DB: PDB REMARK 900 HOLOENZYME DBREF1 5D5S A 1 398 UNP A0A0A5P8W7_CITFR DBREF2 5D5S A A0A0A5P8W7 1 398 SEQADV 5D5S ALA A 339 UNP A0A0A5P8W SER 339 ENGINEERED MUTATION SEQRES 1 A 398 MET SER ASP CSO ARG THR TYR GLY PHE ASN THR GLN ILE SEQRES 2 A 398 VAL HIS ALA GLY GLN GLN PRO ASP PRO SER THR GLY ALA SEQRES 3 A 398 LEU SER THR PRO ILE PHE GLN THR SER THR PHE VAL PHE SEQRES 4 A 398 ASP SER ALA GLU GLN GLY ALA ALA ARG PHE ALA LEU GLU SEQRES 5 A 398 GLU SER GLY TYR ILE TYR THR ARG LEU GLY ASN PRO THR SEQRES 6 A 398 THR ASP ALA LEU GLU LYS LYS LEU ALA VAL LEU GLU ARG SEQRES 7 A 398 GLY GLU ALA GLY LEU ALA THR ALA SER GLY ILE SER ALA SEQRES 8 A 398 ILE THR THR THR LEU LEU THR LEU CYS GLN GLN GLY ASP SEQRES 9 A 398 HIS ILE VAL SER ALA SER ALA ILE TYR GLY CYS THR HIS SEQRES 10 A 398 ALA PHE LEU SER HIS SER MET PRO LYS PHE GLY ILE ASN SEQRES 11 A 398 VAL SER PHE VAL ASP ALA ALA LYS PRO GLU GLU ILE ARG SEQRES 12 A 398 ALA ALA MET ARG PRO GLU THR LYS VAL VAL TYR ILE GLU SEQRES 13 A 398 THR PRO ALA ASN PRO THR LEU SER LEU VAL ASP ILE GLU SEQRES 14 A 398 THR VAL ALA GLY ILE ALA HIS GLN GLN GLY ALA LEU LEU SEQRES 15 A 398 VAL VAL ASP ASN THR PHE MET SER PRO TYR CSO GLN GLN SEQRES 16 A 398 PRO LEU GLN LEU GLY ALA ASP ILE VAL VAL HIS SER VAL SEQRES 17 A 398 THR LYS TYR ILE ASN GLY HIS GLY ASP VAL ILE GLY GLY SEQRES 18 A 398 ILE ILE VAL GLY LYS GLN GLU PHE ILE ASP GLN ALA ARG SEQRES 19 A 398 PHE VAL GLY LEU LYS ASP ILE THR GLY GLY CSO MET SER SEQRES 20 A 398 PRO PHE ASN ALA TRP LEU THR LEU ARG GLY VAL LYS THR SEQRES 21 A 398 LEU GLY ILE ARG MET GLU ARG HIS CYS GLU ASN ALA LEU SEQRES 22 A 398 LYS ILE ALA ARG PHE LEU GLU GLY HIS PRO SER ILE THR SEQRES 23 A 398 ARG VAL TYR TYR PRO GLY LEU SER SER HIS PRO GLN TYR SEQRES 24 A 398 GLU LEU GLY GLN ARG GLN MET SER LEU PRO GLY GLY ILE SEQRES 25 A 398 ILE SER PHE GLU ILE ALA GLY GLY LEU GLU ALA GLY ARG SEQRES 26 A 398 ARG MET ILE ASN SER VAL GLU LEU CYS LEU LEU ALA VAL SEQRES 27 A 398 ALA LEU GLY ASP THR GLU THR LEU ILE GLN HIS PRO ALA SEQRES 28 A 398 SER MET THR HIS SER PRO VAL ALA PRO GLU GLU ARG LEU SEQRES 29 A 398 LYS ALA GLY ILE THR ASP GLY LEU ILE ARG LEU SER VAL SEQRES 30 A 398 GLY LEU GLU ASP PRO GLU ASP ILE ILE ASN ASP LEU GLU SEQRES 31 A 398 HIS ALA ILE ARG LYS ALA THR PHE MODRES 5D5S CSO A 4 CYS MODIFIED RESIDUE MODRES 5D5S CSO A 193 CYS MODIFIED RESIDUE MODRES 5D5S CSO A 245 CYS MODIFIED RESIDUE HET CSO A 4 7 HET CSO A 193 7 HET CSO A 245 7 HET PEG A 401 7 HET NA A 402 1 HET PLP A 403 15 HETNAM CSO S-HYDROXYCYSTEINE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NA SODIUM ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 CSO 3(C3 H7 N O3 S) FORMUL 2 PEG C4 H10 O3 FORMUL 3 NA NA 1+ FORMUL 4 PLP C8 H10 N O6 P FORMUL 5 HOH *393(H2 O) HELIX 1 AA1 ASP A 3 TYR A 7 5 5 HELIX 2 AA2 GLY A 8 ALA A 16 1 9 HELIX 3 AA3 ASN A 63 ARG A 78 1 16 HELIX 4 AA4 SER A 87 CYS A 100 1 14 HELIX 5 AA5 TYR A 113 HIS A 122 1 10 HELIX 6 AA6 HIS A 122 PHE A 127 1 6 HELIX 7 AA7 LYS A 138 MET A 146 1 9 HELIX 8 AA8 ASP A 167 GLN A 178 1 12 HELIX 9 AA9 GLN A 195 GLY A 200 5 6 HELIX 10 AB1 LYS A 226 VAL A 236 1 11 HELIX 11 AB2 VAL A 236 ILE A 241 1 6 HELIX 12 AB3 SER A 247 LYS A 259 1 13 HELIX 13 AB4 THR A 260 GLY A 281 1 22 HELIX 14 AB5 GLN A 298 MET A 306 1 9 HELIX 15 AB6 GLY A 319 ASN A 329 1 11 HELIX 16 AB7 ALA A 359 LYS A 365 1 7 HELIX 17 AB8 ASP A 381 THR A 397 1 17 SHEET 1 AA1 7 ALA A 81 THR A 85 0 SHEET 2 AA1 7 GLY A 221 GLY A 225 -1 O GLY A 221 N THR A 85 SHEET 3 AA1 7 ILE A 203 SER A 207 -1 N VAL A 204 O VAL A 224 SHEET 4 AA1 7 LEU A 181 ASP A 185 1 N VAL A 184 O ILE A 203 SHEET 5 AA1 7 THR A 150 GLU A 156 1 N VAL A 153 O VAL A 183 SHEET 6 AA1 7 HIS A 105 ALA A 109 1 N HIS A 105 O LYS A 151 SHEET 7 AA1 7 ASN A 130 VAL A 134 1 O SER A 132 N SER A 108 SHEET 1 AA2 5 ILE A 285 TYR A 289 0 SHEET 2 AA2 5 ILE A 312 ILE A 317 -1 O SER A 314 N TYR A 289 SHEET 3 AA2 5 LEU A 372 SER A 376 -1 O ILE A 373 N PHE A 315 SHEET 4 AA2 5 LEU A 346 GLN A 348 -1 N LEU A 346 O SER A 376 SHEET 5 AA2 5 LEU A 335 LEU A 336 1 N LEU A 335 O ILE A 347 LINK C ASP A 3 N CSO A 4 1555 1555 1.33 LINK C CSO A 4 N ARG A 5 1555 1555 1.33 LINK C TYR A 192 N CSO A 193 1555 1555 1.33 LINK C CSO A 193 N GLN A 194 1555 1555 1.33 LINK NZ LYS A 210 C4A PLP A 403 1555 1555 1.45 LINK C GLY A 244 N CSO A 245 1555 1555 1.33 LINK C CSO A 245 N MET A 246 1555 1555 1.32 LINK OE2 GLU A 344 NA NA A 402 1555 2555 3.13 LINK NA NA A 402 O HOH A 515 1555 1555 2.32 LINK NA NA A 402 O HOH A 520 1555 1555 2.39 LINK NA NA A 402 O HOH A 620 1555 2555 3.01 CISPEP 1 GLY A 62 ASN A 63 0 -5.69 CISPEP 2 THR A 157 PRO A 158 0 -6.67 CISPEP 3 ASN A 160 PRO A 161 0 0.41 SITE 1 AC1 5 TYR A 192 ARG A 304 MET A 306 SER A 307 SITE 2 AC1 5 HOH A 507 SITE 1 AC2 6 GLN A 18 LYS A 259 GLU A 344 HOH A 515 SITE 2 AC2 6 HOH A 520 HOH A 620 SITE 1 AC3 10 SER A 87 GLY A 88 ILE A 89 TYR A 113 SITE 2 AC3 10 ASP A 185 PHE A 188 SER A 207 THR A 209 SITE 3 AC3 10 LYS A 210 GLY A 220 CRYST1 56.659 123.090 128.785 90.00 90.00 90.00 I 2 2 2 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 0.017649 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008124 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007765 0.00000