HEADER TRANSFERASE 10-SEP-17 5YD2 TITLE CRYSTAL STRUCTURE OF DELTA 4 MUTANT OF EHPSAT (PHOSPHOSERINE TITLE 2 AMINOTRANSFERASE OF ENTAMOEBA HISTOLYTICA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOSERINE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTAMOEBA HISTOLYTICA HM-3:IMSS; SOURCE 3 ORGANISM_TAXID: 885315; SOURCE 4 GENE: KM1_040390; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET21C KEYWDS DELTA4_EHPSAT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.SINGH,S.GOURINATH REVDAT 3 22-NOV-23 5YD2 1 REMARK REVDAT 2 10-JUL-19 5YD2 1 JRNL REVDAT 1 31-OCT-18 5YD2 0 JRNL AUTH R.K.SINGH,P.TOMAR,S.DHARAVATH,S.KUMAR,S.GOURINATH JRNL TITL N-TERMINAL RESIDUES ARE CRUCIAL FOR QUATERNARY STRUCTURE AND JRNL TITL 2 ACTIVE SITE CONFORMATION FOR THE PHOSPHOSERINE JRNL TITL 3 AMINOTRANSFERASE FROM ENTERIC HUMAN PARASITE E. HISTOLYTICA. JRNL REF INT.J.BIOL.MACROMOL. V. 132 1012 2019 JRNL REFN ISSN 0141-8130 JRNL PMID 30959130 JRNL DOI 10.1016/J.IJBIOMAC.2019.04.027 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 29564 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) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1576 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5539 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.32000 REMARK 3 B22 (A**2) : 2.27000 REMARK 3 B33 (A**2) : -1.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -2.98000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.493 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.275 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5672 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5585 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7646 ; 1.548 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12875 ; 1.022 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 693 ; 6.849 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 245 ;36.333 ;25.143 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1082 ;15.624 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;13.101 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 857 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6301 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1245 ; 0.004 ; 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): 2778 ; 3.218 ; 4.045 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2777 ; 3.217 ; 4.045 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3469 ; 5.004 ; 6.057 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3470 ; 5.004 ; 6.057 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2894 ; 3.284 ; 4.388 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2895 ; 3.284 ; 4.388 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4178 ; 5.119 ; 6.407 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6510 ; 7.649 ;32.091 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6508 ; 7.648 ;32.091 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 7 351 B 7 351 20923 0.12 0.05 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 6 A 516 REMARK 3 ORIGIN FOR THE GROUP (A): -24.5498 34.2783 112.0261 REMARK 3 T TENSOR REMARK 3 T11: 0.2027 T22: 0.3685 REMARK 3 T33: 0.0843 T12: -0.0365 REMARK 3 T13: -0.1218 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 0.5907 L22: 0.4106 REMARK 3 L33: 0.7904 L12: 0.1905 REMARK 3 L13: 0.4558 L23: 0.4173 REMARK 3 S TENSOR REMARK 3 S11: -0.0293 S12: -0.0599 S13: 0.0055 REMARK 3 S21: -0.0759 S22: -0.0098 S23: 0.0552 REMARK 3 S31: -0.0791 S32: 0.1414 S33: 0.0391 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 7 B 508 REMARK 3 ORIGIN FOR THE GROUP (A): -54.7130 20.1781 109.0331 REMARK 3 T TENSOR REMARK 3 T11: 0.2178 T22: 0.3498 REMARK 3 T33: 0.1601 T12: -0.0443 REMARK 3 T13: -0.1863 T23: 0.0534 REMARK 3 L TENSOR REMARK 3 L11: 1.0106 L22: 0.1127 REMARK 3 L33: 0.3907 L12: 0.0859 REMARK 3 L13: -0.1640 L23: -0.1873 REMARK 3 S TENSOR REMARK 3 S11: 0.1036 S12: -0.3911 S13: -0.1067 REMARK 3 S21: -0.1074 S22: 0.0136 S23: 0.0932 REMARK 3 S31: 0.1171 S32: -0.1388 S33: -0.1171 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YD2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 77.15 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : CU-NI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31390 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 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: DM REMARK 200 STARTING MODEL: 5YB0 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG2000MME 100 MM TRIS PH-8.5 200 REMARK 280 MM TMAO, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 66.11900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.95200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 66.11900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.95200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ARG A 3 REMARK 465 GLN A 4 REMARK 465 ASN A 5 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 ARG B 3 REMARK 465 GLN B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 THR B 353 REMARK 465 HIS B 354 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 NZ LYS A 187 O4A PLP A 402 2.19 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 ASN A 86 -62.54 -91.43 REMARK 500 LYS A 87 -63.53 -101.17 REMARK 500 GLN A 186 33.27 -82.27 REMARK 500 LYS A 187 71.29 -158.58 REMARK 500 ASN A 188 -46.72 124.03 REMARK 500 SER A 321 -31.04 -38.89 REMARK 500 ASN B 8 -22.38 -147.49 REMARK 500 PRO B 61 -179.92 -69.66 REMARK 500 ASN B 86 -62.86 -92.06 REMARK 500 LYS B 87 -63.18 -100.79 REMARK 500 LYS B 187 -77.21 -83.68 REMARK 500 ASN B 188 -144.88 -90.69 REMARK 500 CYS B 189 -31.18 55.98 REMARK 500 SER B 321 -32.84 -38.48 REMARK 500 ILE B 329 59.74 -97.85 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 GLU A 349 GLN A 350 146.97 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 CL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP B 402 DBREF 5YD2 A 1 354 UNP M7XC02 M7XC02_ENTHI 1 358 DBREF 5YD2 B 1 354 UNP M7XC02 M7XC02_ENTHI 1 358 SEQADV 5YD2 A UNP M7XC02 ALA 11 DELETION SEQADV 5YD2 A UNP M7XC02 GLY 12 DELETION SEQADV 5YD2 A UNP M7XC02 PRO 13 DELETION SEQADV 5YD2 A UNP M7XC02 ALA 14 DELETION SEQADV 5YD2 B UNP M7XC02 ALA 11 DELETION SEQADV 5YD2 B UNP M7XC02 GLY 12 DELETION SEQADV 5YD2 B UNP M7XC02 PRO 13 DELETION SEQADV 5YD2 B UNP M7XC02 ALA 14 DELETION SEQRES 1 A 354 MET GLU ARG GLN ASN ILE HIS ASN PHE GLY ALA MET ALA SEQRES 2 A 354 LYS GLU VAL ILE GLU ALA THR ALA LYS ALA VAL ASN ASN SEQRES 3 A 354 PHE TRP GLU GLY LEU SER ILE LEU GLU ILE SER HIS ARG SEQRES 4 A 354 SER LYS GLU TRP ILE ASN VAL MET ASN GLU THR LYS ALA SEQRES 5 A 354 LEU MET LYS GLU VAL MET ASP ILE PRO GLU GLY TYR GLU SEQRES 6 A 354 ILE LEU PHE PHE GLY GLY GLY ALA SER LEU GLN PHE LEU SEQRES 7 A 354 MET VAL ALA MET ASN LEU LEU ASN LYS LYS ALA CYS TYR SEQRES 8 A 354 LEU ASP THR GLY VAL TRP ALA SER LYS ALA ILE LYS GLU SEQRES 9 A 354 ALA GLU ASN ILE GLY GLU VAL LYS ILE ILE GLY THR SER SEQRES 10 A 354 LYS ASP LYS ASN TYR THR TYR ILE PRO GLU TYR GLN ILE SEQRES 11 A 354 PRO SER ASP TYR ASP TYR PHE HIS ILE THR THR ASN ASN SEQRES 12 A 354 THR ILE TYR GLY THR GLU ILE ARG LYS ASP ILE GLU SER SEQRES 13 A 354 PRO ILE PRO LEU VAL ALA ASP MET SER SER ASP ILE LEU SEQRES 14 A 354 SER LYS PRO ILE ASP ILE SER LYS TYR SER LEU ILE TYR SEQRES 15 A 354 ALA GLY ALA GLN LYS ASN CYS GLY ALA ALA GLY VAL THR SEQRES 16 A 354 ILE VAL ILE ILE LYS LYS GLU ILE LEU GLY LYS VAL GLN SEQRES 17 A 354 ARG LYS ILE PRO ILE ILE LEU ASP TYR GLN VAL HIS ILE SEQRES 18 A 354 LEU ASN ASN SER MET TYR ASN THR PRO PRO VAL ILE SER SEQRES 19 A 354 ILE PHE THR VAL ASN GLN THR LEU LYS TYR ILE LYS LYS SEQRES 20 A 354 ILE GLY GLY LEU LYS LYS ILE GLN GLU LEU ASN GLU GLU SEQRES 21 A 354 LYS ALA ARG LEU LEU TYR ALA GLU ILE ASP ARG ASN LYS SEQRES 22 A 354 ILE PHE ARG GLY THR VAL ARG LYS LYS ASP ARG SER ILE SEQRES 23 A 354 MET ASN VAL CYS PHE VAL MET GLU GLU GLN TYR LYS GLN SEQRES 24 A 354 LEU GLU ASN GLU PHE SER GLU TYR ALA LEU GLN LYS GLY SEQRES 25 A 354 ILE ILE GLY ILE LYS GLY HIS ARG SER VAL GLY GLY PHE SEQRES 26 A 354 ARG ALA SER ILE TYR ASN ALA VAL THR ILE GLU SER VAL SEQRES 27 A 354 GLN ALA LEU ILE LYS CYS MET HIS ASP PHE GLU GLN LEU SEQRES 28 A 354 HIS THR HIS SEQRES 1 B 354 MET GLU ARG GLN ASN ILE HIS ASN PHE GLY ALA MET ALA SEQRES 2 B 354 LYS GLU VAL ILE GLU ALA THR ALA LYS ALA VAL ASN ASN SEQRES 3 B 354 PHE TRP GLU GLY LEU SER ILE LEU GLU ILE SER HIS ARG SEQRES 4 B 354 SER LYS GLU TRP ILE ASN VAL MET ASN GLU THR LYS ALA SEQRES 5 B 354 LEU MET LYS GLU VAL MET ASP ILE PRO GLU GLY TYR GLU SEQRES 6 B 354 ILE LEU PHE PHE GLY GLY GLY ALA SER LEU GLN PHE LEU SEQRES 7 B 354 MET VAL ALA MET ASN LEU LEU ASN LYS LYS ALA CYS TYR SEQRES 8 B 354 LEU ASP THR GLY VAL TRP ALA SER LYS ALA ILE LYS GLU SEQRES 9 B 354 ALA GLU ASN ILE GLY GLU VAL LYS ILE ILE GLY THR SER SEQRES 10 B 354 LYS ASP LYS ASN TYR THR TYR ILE PRO GLU TYR GLN ILE SEQRES 11 B 354 PRO SER ASP TYR ASP TYR PHE HIS ILE THR THR ASN ASN SEQRES 12 B 354 THR ILE TYR GLY THR GLU ILE ARG LYS ASP ILE GLU SER SEQRES 13 B 354 PRO ILE PRO LEU VAL ALA ASP MET SER SER ASP ILE LEU SEQRES 14 B 354 SER LYS PRO ILE ASP ILE SER LYS TYR SER LEU ILE TYR SEQRES 15 B 354 ALA GLY ALA GLN LYS ASN CYS GLY ALA ALA GLY VAL THR SEQRES 16 B 354 ILE VAL ILE ILE LYS LYS GLU ILE LEU GLY LYS VAL GLN SEQRES 17 B 354 ARG LYS ILE PRO ILE ILE LEU ASP TYR GLN VAL HIS ILE SEQRES 18 B 354 LEU ASN ASN SER MET TYR ASN THR PRO PRO VAL ILE SER SEQRES 19 B 354 ILE PHE THR VAL ASN GLN THR LEU LYS TYR ILE LYS LYS SEQRES 20 B 354 ILE GLY GLY LEU LYS LYS ILE GLN GLU LEU ASN GLU GLU SEQRES 21 B 354 LYS ALA ARG LEU LEU TYR ALA GLU ILE ASP ARG ASN LYS SEQRES 22 B 354 ILE PHE ARG GLY THR VAL ARG LYS LYS ASP ARG SER ILE SEQRES 23 B 354 MET ASN VAL CYS PHE VAL MET GLU GLU GLN TYR LYS GLN SEQRES 24 B 354 LEU GLU ASN GLU PHE SER GLU TYR ALA LEU GLN LYS GLY SEQRES 25 B 354 ILE ILE GLY ILE LYS GLY HIS ARG SER VAL GLY GLY PHE SEQRES 26 B 354 ARG ALA SER ILE TYR ASN ALA VAL THR ILE GLU SER VAL SEQRES 27 B 354 GLN ALA LEU ILE LYS CYS MET HIS ASP PHE GLU GLN LEU SEQRES 28 B 354 HIS THR HIS HET CL A 401 1 HET PLP A 402 16 HET CL B 401 1 HET PLP B 402 16 HETNAM CL CHLORIDE ION HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 CL 2(CL 1-) FORMUL 4 PLP 2(C8 H10 N O6 P) FORMUL 7 HOH *24(H2 O) HELIX 1 AA1 ALA A 13 ASN A 26 1 14 HELIX 2 AA2 SER A 40 ASP A 59 1 20 HELIX 3 AA3 GLY A 72 LEU A 85 1 14 HELIX 4 AA4 GLY A 95 ASN A 107 1 13 HELIX 5 AA5 LYS A 118 ASN A 121 5 4 HELIX 6 AA6 ASP A 174 TYR A 178 5 5 HELIX 7 AA7 GLU A 202 LEU A 204 5 3 HELIX 8 AA8 PRO A 212 LEU A 215 5 4 HELIX 9 AA9 ASP A 216 ASN A 223 1 8 HELIX 10 AB1 PRO A 231 ILE A 248 1 18 HELIX 11 AB2 GLY A 249 ASN A 272 1 24 HELIX 12 AB3 ARG A 280 ARG A 284 5 5 HELIX 13 AB4 GLU A 295 GLN A 299 5 5 HELIX 14 AB5 LEU A 300 LYS A 311 1 12 HELIX 15 AB6 THR A 334 ASP A 347 1 14 HELIX 16 AB7 ALA B 13 ASN B 26 1 14 HELIX 17 AB8 SER B 40 ASP B 59 1 20 HELIX 18 AB9 GLY B 72 LEU B 85 1 14 HELIX 19 AC1 GLY B 95 ASN B 107 1 13 HELIX 20 AC2 LYS B 118 ASN B 121 5 4 HELIX 21 AC3 ASP B 174 TYR B 178 5 5 HELIX 22 AC4 GLU B 202 LEU B 204 5 3 HELIX 23 AC5 PRO B 212 LEU B 215 5 4 HELIX 24 AC6 ASP B 216 ASN B 223 1 8 HELIX 25 AC7 PRO B 231 ILE B 248 1 18 HELIX 26 AC8 GLY B 249 ASN B 272 1 24 HELIX 27 AC9 ARG B 280 ARG B 284 5 5 HELIX 28 AD1 GLU B 295 GLN B 299 5 5 HELIX 29 AD2 LEU B 300 LYS B 311 1 12 HELIX 30 AD3 HIS B 319 GLY B 323 5 5 HELIX 31 AD4 THR B 334 HIS B 352 1 19 SHEET 1 AA1 7 TYR A 64 GLY A 70 0 SHEET 2 AA1 7 VAL A 194 LYS A 200 -1 O ILE A 199 N GLU A 65 SHEET 3 AA1 7 LEU A 180 GLY A 184 -1 N ILE A 181 O ILE A 198 SHEET 4 AA1 7 LEU A 160 ASP A 163 1 N ALA A 162 O LEU A 180 SHEET 5 AA1 7 PHE A 137 THR A 140 1 N PHE A 137 O VAL A 161 SHEET 6 AA1 7 LYS A 88 ASP A 93 1 N CYS A 90 O HIS A 138 SHEET 7 AA1 7 GLU A 110 THR A 116 1 O GLY A 115 N ASP A 93 SHEET 1 AA2 2 ASN A 142 ASN A 143 0 SHEET 2 AA2 2 THR A 148 GLU A 149 -1 O THR A 148 N ASN A 143 SHEET 1 AA3 3 PHE A 275 GLY A 277 0 SHEET 2 AA3 3 ASN A 288 MET A 293 -1 O VAL A 292 N ARG A 276 SHEET 3 AA3 3 PHE A 325 SER A 328 -1 O ALA A 327 N VAL A 289 SHEET 1 AA4 7 TYR B 64 GLY B 70 0 SHEET 2 AA4 7 VAL B 194 LYS B 200 -1 O VAL B 197 N LEU B 67 SHEET 3 AA4 7 LEU B 180 GLY B 184 -1 N ILE B 181 O ILE B 198 SHEET 4 AA4 7 LEU B 160 ASP B 163 1 N ALA B 162 O LEU B 180 SHEET 5 AA4 7 PHE B 137 THR B 140 1 N PHE B 137 O VAL B 161 SHEET 6 AA4 7 LYS B 88 ASP B 93 1 N CYS B 90 O HIS B 138 SHEET 7 AA4 7 GLU B 110 THR B 116 1 O GLY B 115 N ASP B 93 SHEET 1 AA5 2 ASN B 142 ASN B 143 0 SHEET 2 AA5 2 THR B 148 GLU B 149 -1 O THR B 148 N ASN B 143 SHEET 1 AA6 3 PHE B 275 GLY B 277 0 SHEET 2 AA6 3 ASN B 288 MET B 293 -1 O VAL B 292 N ARG B 276 SHEET 3 AA6 3 PHE B 325 SER B 328 -1 O ALA B 327 N VAL B 289 SITE 1 AC1 6 GLY A 95 VAL A 96 ASN A 143 THR A 144 SITE 2 AC1 6 ILE A 145 HOH A 505 SITE 1 AC2 10 GLY A 72 ALA A 73 SER A 74 TRP A 97 SITE 2 AC2 10 THR A 144 ASP A 163 SER A 165 LYS A 187 SITE 3 AC2 10 ASN B 228 THR B 229 SITE 1 AC3 4 VAL B 96 TRP B 97 THR B 144 ILE B 145 SITE 1 AC4 11 ASN A 228 THR A 229 GLY B 72 ALA B 73 SITE 2 AC4 11 SER B 74 TRP B 97 THR B 144 ASP B 163 SITE 3 AC4 11 SER B 165 SER B 166 LYS B 187 CRYST1 132.238 67.904 95.030 90.00 110.93 90.00 C 1 2 1 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 0.007562 0.000000 0.002892 0.00000 SCALE2 0.000000 0.014727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011266 0.00000