HEADER LYASE 01-JUL-16 5GJP TITLE CRYSTAL STRUCTURE OF SRLDC IN COMPLEX WITH PLP AND CADAVERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE/ORNITHINE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LDC, PLP BINDING BARREL DOMAIN; COMPND 5 EC: 4.1.1.18; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SELENOMONAS RUMINANTIUM; SOURCE 3 ORGANISM_TAXID: 971; SOURCE 4 STRAIN: ATCC12561; SOURCE 5 GENE: LDC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21T1R; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS BARREL DOMAIN, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-Y.SAGONG,K.-J.KIM REVDAT 4 08-NOV-23 5GJP 1 REMARK REVDAT 3 09-SEP-20 5GJP 1 TITLE REVDAT 2 19-JUL-17 5GJP 1 JRNL REMARK REVDAT 1 23-NOV-16 5GJP 0 JRNL AUTH H.-Y.SAGONG,H.F.SON,S.KIM,Y.-H.KIM,I.-K.KIM,K.-J.KIM JRNL TITL CRYSTAL STRUCTURE AND PYRIDOXAL 5-PHOSPHATE BINDING PROPERTY JRNL TITL 2 OF LYSINE DECARBOXYLASE FROM SELENOMONAS RUMINANTIUM JRNL REF PLOS ONE V. 11 66667 2016 JRNL REFN ESSN 1932-6203 JRNL PMID 27861532 JRNL DOI 10.1371/JOURNAL.PONE.0166667 REMARK 2 REMARK 2 RESOLUTION. 2.50 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 13670 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 958 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 55 REMARK 3 BIN FREE R VALUE : 0.2910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2948 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.45000 REMARK 3 B22 (A**2) : 1.45000 REMARK 3 B33 (A**2) : -4.70000 REMARK 3 B12 (A**2) : 0.72000 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): 0.679 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.335 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.233 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3054 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2910 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4122 ; 1.636 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6711 ; 1.015 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 6.892 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;34.543 ;23.985 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;17.295 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;18.140 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 449 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3415 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 671 ; 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): 1523 ; 3.547 ; 4.912 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1524 ; 3.546 ; 4.913 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1899 ; 5.361 ; 7.357 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5GJP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1300000909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14439 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 24.20 REMARK 200 R MERGE (I) : 0.13200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 12.90 REMARK 200 R MERGE FOR SHELL (I) : 0.31700 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: MOLREP REMARK 200 STARTING MODEL: 5GJN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, SODIUM PHOSPHATE, NACL, PH REMARK 280 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 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 56.48800 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 56.48800 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 56.48800 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 0.00000 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 0.00000 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 56.48800 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 56.48800 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 56.48800 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: 9840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 ASN A 142 REMARK 465 LYS A 143 REMARK 465 ALA A 144 REMARK 465 LEU A 145 REMARK 465 VAL A 146 REMARK 465 ASP A 147 REMARK 465 LEU A 148 REMARK 465 ASN A 149 REMARK 465 LYS A 390 REMARK 465 ALA A 391 REMARK 465 ALA A 392 REMARK 465 VAL A 393 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 OD1 ASP A 117 OG SER A 119 1.85 REMARK 500 OG SER A 182 O1P PLP A 402 2.00 REMARK 500 OD1 ASP A 117 N SER A 119 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 MET A 207 1.93 -69.96 REMARK 500 ASP A 224 -164.58 -116.36 REMARK 500 THR A 353 -84.88 -116.91 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 ASP A 249 THR A 250 -149.13 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 538 DISTANCE = 5.97 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N2P 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 GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GJM RELATED DB: PDB REMARK 900 RELATED ID: 5GJN RELATED DB: PDB REMARK 900 RELATED ID: 5GJO RELATED DB: PDB DBREF 5GJP A 1 393 UNP O50657 DCLO_SELRU 1 393 SEQRES 1 A 393 MET LYS ASN PHE ARG LEU SER GLU LYS GLU VAL LYS THR SEQRES 2 A 393 LEU ALA LYS ARG ILE PRO THR PRO PHE LEU VAL ALA SER SEQRES 3 A 393 LEU ASP LYS VAL GLU GLU ASN TYR GLN PHE MET ARG ARG SEQRES 4 A 393 HIS LEU PRO ARG ALA GLY VAL PHE TYR ALA MET LYS ALA SEQRES 5 A 393 ASN PRO THR PRO GLU ILE LEU SER LEU LEU ALA GLY LEU SEQRES 6 A 393 GLY SER HIS PHE ASP VAL ALA SER ALA GLY GLU MET GLU SEQRES 7 A 393 ILE LEU HIS GLU LEU GLY VAL ASP GLY SER GLN MET ILE SEQRES 8 A 393 TYR ALA ASN PRO VAL LYS ASP ALA ARG GLY LEU LYS ALA SEQRES 9 A 393 ALA ALA ASP TYR ASN VAL ARG ARG PHE THR PHE ASP ASP SEQRES 10 A 393 PRO SER GLU ILE ASP LYS MET ALA LYS ALA VAL PRO GLY SEQRES 11 A 393 ALA ASP VAL LEU VAL ARG ILE ALA VAL ARG ASN ASN LYS SEQRES 12 A 393 ALA LEU VAL ASP LEU ASN THR LYS PHE GLY ALA PRO VAL SEQRES 13 A 393 GLU GLU ALA LEU ASP LEU LEU LYS ALA ALA GLN ASP ALA SEQRES 14 A 393 GLY LEU HIS ALA MET GLY ILE CYS PHE HIS VAL GLY SER SEQRES 15 A 393 GLN SER LEU SER THR ALA ALA TYR GLU GLU ALA LEU LEU SEQRES 16 A 393 VAL ALA ARG ARG LEU PHE ASP GLU ALA GLU GLU MET GLY SEQRES 17 A 393 MET HIS LEU THR ASP LEU ASP ILE GLY GLY GLY PHE PRO SEQRES 18 A 393 VAL PRO ASP ALA LYS GLY LEU ASN VAL ASP LEU ALA ALA SEQRES 19 A 393 MET MET GLU ALA ILE ASN LYS GLN ILE ASP ARG LEU PHE SEQRES 20 A 393 PRO ASP THR ALA VAL TRP THR GLU PRO GLY ARG TYR MET SEQRES 21 A 393 CYS GLY THR ALA VAL ASN LEU VAL THR SER VAL ILE GLY SEQRES 22 A 393 THR LYS THR ARG GLY GLU GLN PRO TRP TYR ILE LEU ASP SEQRES 23 A 393 GLU GLY ILE TYR GLY CYS PHE SER GLY ILE MET TYR ASP SEQRES 24 A 393 HIS TRP THR TYR PRO LEU HIS CYS PHE GLY LYS GLY ASN SEQRES 25 A 393 LYS LYS PRO SER THR PHE GLY GLY PRO SER CYS ASP GLY SEQRES 26 A 393 ILE ASP VAL LEU TYR ARG ASP PHE MET ALA PRO GLU LEU SEQRES 27 A 393 LYS ILE GLY ASP LYS VAL LEU VAL THR GLU MET GLY SER SEQRES 28 A 393 TYR THR SER VAL SER ALA THR ARG PHE ASN GLY PHE TYR SEQRES 29 A 393 LEU ALA PRO THR ILE ILE PHE GLU ASP GLN PRO GLU TYR SEQRES 30 A 393 ALA ALA ARG LEU THR GLU ASP ASP ASP VAL LYS LYS LYS SEQRES 31 A 393 ALA ALA VAL HET N2P A 401 7 HET PLP A 402 16 HET GOL A 403 6 HET GOL A 404 6 HET PGE A 405 10 HET NA A 406 1 HET NA A 407 1 HET MG A 408 1 HETNAM N2P PENTANE-1,5-DIAMINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM GOL GLYCEROL HETNAM PGE TRIETHYLENE GLYCOL HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 N2P C5 H14 N2 FORMUL 3 PLP C8 H10 N O6 P FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 PGE C6 H14 O4 FORMUL 7 NA 2(NA 1+) FORMUL 9 MG MG 2+ FORMUL 10 HOH *38(H2 O) HELIX 1 AA1 SER A 7 ILE A 18 1 12 HELIX 2 AA2 SER A 26 LEU A 41 1 16 HELIX 3 AA3 THR A 55 GLY A 66 1 12 HELIX 4 AA4 SER A 73 LEU A 83 1 11 HELIX 5 AA5 ASP A 86 SER A 88 5 3 HELIX 6 AA6 ASP A 98 TYR A 108 1 11 HELIX 7 AA7 SER A 119 VAL A 128 1 10 HELIX 8 AA8 GLU A 158 ALA A 169 1 12 HELIX 9 AA9 THR A 187 MET A 207 1 21 HELIX 10 AB1 ASP A 231 PHE A 247 1 17 HELIX 11 AB2 GLY A 257 GLY A 262 1 6 HELIX 12 AB3 GLY A 291 PHE A 293 5 3 HELIX 13 AB4 SER A 294 ASP A 299 1 6 HELIX 14 AB5 THR A 353 ALA A 357 5 5 HELIX 15 AB6 ARG A 359 PHE A 363 5 5 HELIX 16 AB7 GLN A 374 LYS A 388 1 15 SHEET 1 AA1 6 LEU A 305 HIS A 306 0 SHEET 2 AA1 6 LYS A 343 VAL A 346 -1 O LEU A 345 N HIS A 306 SHEET 3 AA1 6 VAL A 265 LYS A 275 -1 N LEU A 267 O VAL A 346 SHEET 4 AA1 6 TRP A 282 LEU A 285 -1 O ILE A 284 N GLY A 273 SHEET 5 AA1 6 LYS A 314 GLY A 319 1 O GLY A 319 N LEU A 285 SHEET 6 AA1 6 VAL A 328 ALA A 335 -1 O LEU A 329 N PHE A 318 SHEET 1 AA2 5 LEU A 305 HIS A 306 0 SHEET 2 AA2 5 LYS A 343 VAL A 346 -1 O LEU A 345 N HIS A 306 SHEET 3 AA2 5 VAL A 265 LYS A 275 -1 N LEU A 267 O VAL A 346 SHEET 4 AA2 5 PHE A 22 ALA A 25 -1 N PHE A 22 O VAL A 268 SHEET 5 AA2 5 THR A 368 ILE A 370 1 O ILE A 369 N LEU A 23 SHEET 1 AA3 9 ALA A 44 ALA A 49 0 SHEET 2 AA3 9 HIS A 68 VAL A 71 1 O HIS A 68 N TYR A 48 SHEET 3 AA3 9 MET A 90 TYR A 92 1 O ILE A 91 N VAL A 71 SHEET 4 AA3 9 ARG A 112 PHE A 115 1 O ARG A 112 N TYR A 92 SHEET 5 AA3 9 ASP A 132 ARG A 136 1 O ARG A 136 N PHE A 115 SHEET 6 AA3 9 HIS A 172 CYS A 177 1 O CYS A 177 N VAL A 135 SHEET 7 AA3 9 ASP A 213 ASP A 215 1 O ASP A 215 N ILE A 176 SHEET 8 AA3 9 ALA A 251 THR A 254 1 O ALA A 251 N LEU A 214 SHEET 9 AA3 9 ALA A 44 ALA A 49 1 N PHE A 47 O THR A 254 CISPEP 1 THR A 20 PRO A 21 0 -5.81 CISPEP 2 GLY A 278 GLU A 279 0 -6.43 SITE 1 AC1 8 SER A 182 ARG A 258 TYR A 290 TYR A 298 SITE 2 AC1 8 ASP A 299 ASP A 324 TYR A 352 PLP A 402 SITE 1 AC2 13 LYS A 51 ASP A 70 HIS A 179 SER A 182 SITE 2 AC2 13 GLY A 218 GLY A 219 GLU A 255 GLY A 257 SITE 3 AC2 13 ARG A 258 CYS A 323 TYR A 352 N2P A 401 SITE 4 AC2 13 HOH A 508 SITE 1 AC3 3 ALA A 99 LYS A 123 ILE A 272 SITE 1 AC4 4 LYS A 2 SER A 26 GLU A 32 PGE A 405 SITE 1 AC5 10 MET A 1 LYS A 29 GLU A 32 ASN A 33 SITE 2 AC5 10 PHE A 36 PRO A 223 LEU A 232 TYR A 259 SITE 3 AC5 10 THR A 263 GOL A 404 SITE 1 AC6 1 GLU A 348 SITE 1 AC7 2 ALA A 357 ARG A 359 CRYST1 111.734 111.734 112.976 90.00 90.00 120.00 P 63 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 0.008950 0.005167 0.000000 0.00000 SCALE2 0.000000 0.010334 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008851 0.00000 TER 2949 LYS A 389 HETATM 2950 C1 N2P A 401 -24.124 -24.491 1.049 1.00 57.83 C HETATM 2951 C2 N2P A 401 -24.491 -23.110 1.652 1.00 61.86 C HETATM 2952 C3 N2P A 401 -25.382 -22.207 0.799 1.00 56.99 C HETATM 2953 C4 N2P A 401 -26.382 -21.385 1.597 1.00 61.78 C HETATM 2954 NE2 N2P A 401 -23.540 -25.432 2.070 1.00 56.45 N HETATM 2955 C5 N2P A 401 -27.711 -21.216 0.855 1.00 67.92 C HETATM 2956 N1 N2P A 401 -27.633 -20.811 -0.581 1.00 66.10 N HETATM 2957 N1 PLP A 402 -35.299 -20.528 -1.813 1.00 62.23 N HETATM 2958 C2 PLP A 402 -34.628 -20.854 -2.926 1.00 62.38 C HETATM 2959 C2A PLP A 402 -35.257 -20.725 -4.278 1.00 63.96 C HETATM 2960 C3 PLP A 402 -33.258 -21.350 -2.830 1.00 56.98 C HETATM 2961 O3 PLP A 402 -32.598 -21.660 -3.956 1.00 66.92 O HETATM 2962 C4 PLP A 402 -32.650 -21.472 -1.497 1.00 62.72 C HETATM 2963 C4A PLP A 402 -31.268 -21.964 -1.322 1.00 67.16 C HETATM 2964 O4A PLP A 402 -30.339 -21.188 -1.322 1.00 69.84 O HETATM 2965 C5 PLP A 402 -33.494 -21.075 -0.352 1.00 53.11 C HETATM 2966 C6 PLP A 402 -34.778 -20.633 -0.590 1.00 56.76 C HETATM 2967 C5A PLP A 402 -32.989 -21.170 1.059 1.00 51.35 C HETATM 2968 O4P PLP A 402 -32.583 -19.930 1.599 1.00 44.80 O HETATM 2969 P PLP A 402 -32.094 -19.848 3.098 1.00 39.57 P HETATM 2970 O1P PLP A 402 -31.000 -18.848 3.132 1.00 47.15 O HETATM 2971 O2P PLP A 402 -33.308 -19.426 3.812 1.00 44.75 O HETATM 2972 O3P PLP A 402 -31.647 -21.210 3.405 1.00 38.10 O HETATM 2973 C1 GOL A 403 -12.584 -43.245 19.942 1.00 76.00 C HETATM 2974 O1 GOL A 403 -13.435 -42.594 18.975 1.00 73.42 O HETATM 2975 C2 GOL A 403 -11.645 -42.311 20.683 1.00 74.67 C HETATM 2976 O2 GOL A 403 -12.402 -41.485 21.576 1.00 69.59 O HETATM 2977 C3 GOL A 403 -10.642 -43.165 21.447 1.00 75.80 C HETATM 2978 O3 GOL A 403 -9.796 -43.876 20.533 1.00 79.58 O HETATM 2979 C1 GOL A 404 -37.337 -25.609 23.211 1.00 79.74 C HETATM 2980 O1 GOL A 404 -37.471 -24.453 22.372 1.00 80.25 O HETATM 2981 C2 GOL A 404 -37.126 -26.847 22.331 1.00 81.72 C HETATM 2982 O2 GOL A 404 -38.390 -27.346 21.841 1.00 67.91 O HETATM 2983 C3 GOL A 404 -36.389 -27.934 23.123 1.00 79.26 C HETATM 2984 O3 GOL A 404 -36.655 -29.242 22.591 1.00 73.96 O HETATM 2985 C1 PGE A 405 -38.888 -21.908 19.488 1.00 73.62 C HETATM 2986 O1 PGE A 405 -39.321 -22.660 20.629 1.00 67.02 O HETATM 2987 C2 PGE A 405 -39.799 -20.737 19.073 1.00 72.71 C HETATM 2988 O2 PGE A 405 -39.015 -19.654 18.529 1.00 71.94 O HETATM 2989 C3 PGE A 405 -38.408 -19.924 17.260 1.00 67.86 C HETATM 2990 C4 PGE A 405 -37.543 -18.752 16.801 1.00 73.76 C HETATM 2991 O4 PGE A 405 -33.714 -18.724 15.395 1.00 94.61 O HETATM 2992 C6 PGE A 405 -34.687 -19.433 14.626 1.00 90.11 C HETATM 2993 C5 PGE A 405 -35.836 -19.956 15.497 1.00 84.87 C HETATM 2994 O3 PGE A 405 -36.157 -19.097 16.601 1.00 82.66 O HETATM 2995 NA NA A 406 -26.349 -22.161 22.327 1.00 47.56 NA HETATM 2996 NA NA A 407 -46.583 -42.936 3.280 1.00 54.05 NA HETATM 2997 MG MG A 408 -18.769 -39.323 -1.099 1.00 49.76 MG HETATM 2998 O HOH A 501 -7.922 -37.857 33.391 1.00 54.38 O HETATM 2999 O HOH A 502 -52.389 -5.682 -7.820 1.00 55.66 O HETATM 3000 O HOH A 503 -24.585 -23.935 7.782 1.00 41.97 O HETATM 3001 O HOH A 504 -16.402 -37.083 32.241 1.00 61.18 O HETATM 3002 O HOH A 505 -52.211 -2.415 6.513 1.00 49.25 O HETATM 3003 O HOH A 506 -31.802 -35.733 -8.425 1.00 39.91 O HETATM 3004 O HOH A 507 -28.687 -34.700 5.659 1.00 39.77 O HETATM 3005 O HOH A 508 -34.161 -19.152 6.409 1.00 33.99 O HETATM 3006 O HOH A 509 -40.791 -40.527 7.937 1.00 59.01 O HETATM 3007 O HOH A 510 -21.191 -36.513 8.284 1.00 35.09 O HETATM 3008 O HOH A 511 -33.067 -26.454 7.827 1.00 44.16 O HETATM 3009 O HOH A 512 -27.383 -37.634 8.762 1.00 38.45 O HETATM 3010 O HOH A 513 -23.980 -36.403 8.071 1.00 34.67 O HETATM 3011 O HOH A 514 -48.030 -23.123 3.838 1.00 43.02 O HETATM 3012 O HOH A 515 -30.812 -11.328 -6.289 1.00 46.16 O HETATM 3013 O HOH A 516 -27.714 -30.024 6.678 1.00 32.37 O HETATM 3014 O HOH A 517 -16.826 -42.345 10.324 1.00 44.64 O HETATM 3015 O HOH A 518 -11.507 -20.003 14.185 1.00 50.77 O HETATM 3016 O HOH A 519 -13.249 -18.659 21.877 1.00 54.08 O HETATM 3017 O HOH A 520 -15.239 -42.506 -0.575 1.00 40.77 O HETATM 3018 O HOH A 521 -17.290 -23.911 25.904 1.00 62.25 O HETATM 3019 O HOH A 522 -16.645 -34.624 28.094 1.00 47.22 O HETATM 3020 O HOH A 523 -14.610 -20.189 1.675 1.00 65.78 O HETATM 3021 O HOH A 524 -41.482 -39.743 15.814 1.00 55.12 O HETATM 3022 O HOH A 525 -10.918 -22.363 9.543 1.00 46.81 O HETATM 3023 O HOH A 526 -31.805 -29.896 29.784 1.00 48.42 O HETATM 3024 O HOH A 527 -39.716 -41.501 24.534 1.00 56.22 O HETATM 3025 O HOH A 528 -9.824 -24.013 6.272 1.00 70.07 O HETATM 3026 O HOH A 529 -49.472 -10.810 13.043 1.00 48.53 O HETATM 3027 O HOH A 530 -19.466 -40.510 27.969 1.00 50.12 O HETATM 3028 O HOH A 531 -25.570 -14.819 -0.435 1.00 55.61 O HETATM 3029 O HOH A 532 -48.199 -39.709 -3.151 1.00 48.81 O HETATM 3030 O HOH A 533 -31.603 -38.025 3.645 1.00 76.25 O HETATM 3031 O HOH A 534 -23.197 -15.986 5.124 1.00 54.03 O HETATM 3032 O HOH A 535 -55.533 -10.927 4.580 1.00 47.60 O HETATM 3033 O HOH A 536 -23.605 -14.754 1.679 1.00 46.96 O HETATM 3034 O HOH A 537 -42.530 -39.003 -20.124 1.00 61.75 O HETATM 3035 O HOH A 538 -46.511 -32.517 27.971 1.00 62.34 O CONECT 2950 2951 2954 CONECT 2951 2950 2952 CONECT 2952 2951 2953 CONECT 2953 2952 2955 CONECT 2954 2950 CONECT 2955 2953 2956 CONECT 2956 2955 CONECT 2957 2958 2966 CONECT 2958 2957 2959 2960 CONECT 2959 2958 CONECT 2960 2958 2961 2962 CONECT 2961 2960 CONECT 2962 2960 2963 2965 CONECT 2963 2962 2964 CONECT 2964 2963 CONECT 2965 2962 2966 2967 CONECT 2966 2957 2965 CONECT 2967 2965 2968 CONECT 2968 2967 2969 CONECT 2969 2968 2970 2971 2972 CONECT 2970 2969 CONECT 2971 2969 CONECT 2972 2969 CONECT 2973 2974 2975 CONECT 2974 2973 CONECT 2975 2973 2976 2977 CONECT 2976 2975 CONECT 2977 2975 2978 CONECT 2978 2977 CONECT 2979 2980 2981 CONECT 2980 2979 CONECT 2981 2979 2982 2983 CONECT 2982 2981 CONECT 2983 2981 2984 CONECT 2984 2983 CONECT 2985 2986 2987 CONECT 2986 2985 CONECT 2987 2985 2988 CONECT 2988 2987 2989 CONECT 2989 2988 2990 CONECT 2990 2989 2994 CONECT 2991 2992 CONECT 2992 2991 2993 CONECT 2993 2992 2994 CONECT 2994 2990 2993 MASTER 384 0 8 16 20 0 13 6 3034 1 45 31 END