HEADER PLP-BINDING PROTEIN 05-APR-17 5NM8 TITLE STRUCTURE OF PIPY, THE COG0325 FAMILY MEMBER OF SYNECHOCOCCUS TITLE 2 ELONGATUS PCC7942, WITH PLP BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIPY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS (STRAIN PCC 7942); SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 GENE: SYNPCC7942_2060; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-22B(+)-2060 KEYWDS FOLD TYPE III PLP-PROTEIN, VITAMIN B6, PYRIDOXAL PHOSPHATE, SCHIFF KEYWDS 2 BASE, PLP-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.TREMINO,A.FORCADA-NADAL,A.CONTRERAS,V.RUBIO REVDAT 5 17-JAN-24 5NM8 1 LINK REVDAT 4 08-NOV-17 5NM8 1 JRNL REVDAT 3 27-SEP-17 5NM8 1 JRNL REVDAT 2 20-SEP-17 5NM8 1 AUTHOR REVDAT 1 13-SEP-17 5NM8 0 JRNL AUTH L.TREMINO,A.FORCADA-NADAL,A.CONTRERAS,V.RUBIO JRNL TITL STUDIES ON CYANOBACTERIAL PROTEIN PIPY SHED LIGHT ON JRNL TITL 2 STRUCTURE, POTENTIAL FUNCTIONS, AND VITAMIN B6 -DEPENDENT JRNL TITL 3 EPILEPSY. JRNL REF FEBS LETT. V. 591 3431 2017 JRNL REFN ISSN 1873-3468 JRNL PMID 28914444 JRNL DOI 10.1002/1873-3468.12841 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 35318 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1754 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2540 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3204 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72000 REMARK 3 B22 (A**2) : -0.63000 REMARK 3 B33 (A**2) : -0.09000 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.114 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.848 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3315 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3113 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4516 ; 1.666 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7160 ; 0.994 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 6.061 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;35.890 ;23.359 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 523 ;13.540 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;17.290 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 517 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3711 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 660 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1717 ; 1.646 ; 2.983 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1716 ; 1.642 ; 2.982 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2142 ; 2.544 ; 4.461 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2143 ; 2.544 ; 4.461 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1598 ; 2.155 ; 3.232 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1599 ; 2.154 ; 3.234 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2373 ; 3.342 ; 4.743 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3572 ; 5.395 ;35.750 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3541 ; 5.364 ;35.520 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 : 4 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 3 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): -26.4769 -17.2028 23.4723 REMARK 3 T TENSOR REMARK 3 T11: 0.0452 T22: 0.1953 REMARK 3 T33: 0.0351 T12: 0.0430 REMARK 3 T13: 0.0015 T23: -0.0254 REMARK 3 L TENSOR REMARK 3 L11: 1.0384 L22: 0.7600 REMARK 3 L33: 1.7703 L12: 0.3293 REMARK 3 L13: 0.6747 L23: 0.6359 REMARK 3 S TENSOR REMARK 3 S11: 0.0595 S12: -0.2032 S13: -0.0134 REMARK 3 S21: -0.0545 S22: -0.0442 S23: -0.0513 REMARK 3 S31: -0.0043 S32: -0.3459 S33: -0.0153 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 : A 77 A 219 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5837 -15.9170 11.8052 REMARK 3 T TENSOR REMARK 3 T11: 0.0824 T22: 0.0803 REMARK 3 T33: 0.0681 T12: 0.0244 REMARK 3 T13: -0.0015 T23: -0.0435 REMARK 3 L TENSOR REMARK 3 L11: 0.7732 L22: 0.3507 REMARK 3 L33: 1.5796 L12: 0.2299 REMARK 3 L13: 0.4883 L23: 0.3253 REMARK 3 S TENSOR REMARK 3 S11: -0.0056 S12: -0.0007 S13: -0.1582 REMARK 3 S21: -0.0642 S22: 0.0991 S23: -0.0941 REMARK 3 S31: -0.2655 S32: -0.0489 S33: -0.0934 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 3 B 92 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7823 3.7731 38.5520 REMARK 3 T TENSOR REMARK 3 T11: 0.2048 T22: 0.1170 REMARK 3 T33: 0.2022 T12: -0.0242 REMARK 3 T13: -0.1576 T23: -0.0669 REMARK 3 L TENSOR REMARK 3 L11: 0.1202 L22: 3.6415 REMARK 3 L33: 0.5641 L12: -0.2485 REMARK 3 L13: -0.1675 L23: 1.3606 REMARK 3 S TENSOR REMARK 3 S11: -0.1747 S12: -0.0029 S13: 0.1419 REMARK 3 S21: 0.0660 S22: 0.4905 S23: -0.5869 REMARK 3 S31: 0.1258 S32: 0.1620 S33: -0.3158 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 93 B 217 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5898 -7.8283 47.2612 REMARK 3 T TENSOR REMARK 3 T11: 0.3559 T22: 0.1622 REMARK 3 T33: 0.0652 T12: 0.1675 REMARK 3 T13: 0.0307 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.0217 L22: 2.1161 REMARK 3 L33: 1.3215 L12: -0.2611 REMARK 3 L13: 0.9345 L23: 0.7217 REMARK 3 S TENSOR REMARK 3 S11: -0.2836 S12: -0.2039 S13: -0.1962 REMARK 3 S21: 0.6610 S22: 0.4679 S23: -0.0075 REMARK 3 S31: 0.0339 S32: -0.0174 S33: -0.1843 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 REMARK 4 REMARK 4 5NM8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 71.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.05100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.500 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: PDB FILE 5NLC, CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES-NA PH 7.5 0.2 M CALCIUM REMARK 280 ACETATE 18% (WT/VOL) POLYETHYLENE GLYCOL 8000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.31350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.86850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.46850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.86850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.31350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.46850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ALA A 2 REMARK 465 SER A 220 REMARK 465 LEU A 221 REMARK 465 GLU A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 PRO B 123 REMARK 465 ASN B 124 REMARK 465 LYS B 125 REMARK 465 PRO B 218 REMARK 465 ARG B 219 REMARK 465 SER B 220 REMARK 465 LEU B 221 REMARK 465 GLU B 222 REMARK 465 HIS B 223 REMARK 465 HIS B 224 REMARK 465 HIS B 225 REMARK 465 HIS B 226 REMARK 465 HIS B 227 REMARK 465 HIS B 228 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 GLN A 3 CG CD OE1 NE2 REMARK 470 ASP A 61 CG OD1 OD2 REMARK 470 GLN A 184 CG CD OE1 NE2 REMARK 470 ARG A 219 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 3 CG CD OE1 NE2 REMARK 470 GLU B 6 CG CD OE1 OE2 REMARK 470 GLU B 35 CG CD OE1 OE2 REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 GLN B 74 CG CD OE1 NE2 REMARK 470 ASN B 76 CG OD1 ND2 REMARK 470 GLU B 83 CG CD OE1 OE2 REMARK 470 TRP B 94 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 94 CZ3 CH2 REMARK 470 GLU B 98 CG CD OE1 OE2 REMARK 470 ARG B 99 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 101 CG OD1 OD2 REMARK 470 ARG B 102 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 103 CG1 CG2 CD1 REMARK 470 GLU B 106 CG CD OE1 OE2 REMARK 470 LEU B 107 CG CD1 CD2 REMARK 470 ASP B 122 CG OD1 OD2 REMARK 470 ASP B 129 CG OD1 OD2 REMARK 470 LEU B 133 CG CD1 CD2 REMARK 470 GLU B 136 CG CD OE1 OE2 REMARK 470 PRO B 138 CG CD REMARK 470 GLN B 139 CG CD OE1 NE2 REMARK 470 LEU B 140 CG CD1 CD2 REMARK 470 GLN B 142 CG CD OE1 NE2 REMARK 470 LEU B 143 CG CD1 CD2 REMARK 470 GLN B 145 CG CD OE1 NE2 REMARK 470 LEU B 157 CG CD1 CD2 REMARK 470 GLU B 177 CG CD OE1 OE2 REMARK 470 GLN B 181 CG CD OE1 NE2 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 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 3.7 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 MET A 194 -167.41 -127.42 REMARK 500 LYS B 26 -9.98 -57.46 REMARK 500 LYS B 72 132.81 -36.21 REMARK 500 MET B 194 -169.00 -122.44 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 501 DISTANCE = 5.93 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 CA B 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 469 O REMARK 620 2 HOH A 491 O 76.8 REMARK 620 3 PRO B 63 O 142.0 141.0 REMARK 620 4 HOH B 408 O 143.8 74.4 70.7 REMARK 620 5 HOH B 429 O 72.3 141.4 71.5 142.2 REMARK 620 6 HOH B 433 O 106.5 82.5 81.2 91.0 84.7 REMARK 620 7 HOH B 452 O 69.6 101.2 98.8 95.0 89.2 173.6 REMARK 620 N 1 2 3 4 5 6 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 301 and LYS B REMARK 800 26 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NLC RELATED DB: PDB REMARK 900 5NLC CONTAINS THE SAME PROTEIN WITHOUT PYRIDOXAL 5-PHOSPHATE DBREF 5NM8 A 1 221 UNP Q31LH9 Q31LH9_SYNE7 1 221 DBREF 5NM8 B 1 221 UNP Q31LH9 Q31LH9_SYNE7 1 221 SEQADV 5NM8 GLU A 222 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 223 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 224 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 225 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 226 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 227 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS A 228 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 GLU B 222 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 223 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 224 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 225 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 226 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 227 UNP Q31LH9 EXPRESSION TAG SEQADV 5NM8 HIS B 228 UNP Q31LH9 EXPRESSION TAG SEQRES 1 A 228 MET ALA GLN ILE ALA GLU ARG LEU ALA SER LEU ARG SER SEQRES 2 A 228 GLN LEU PRO PRO SER VAL GLN LEU ILE ALA VAL SER LYS SEQRES 3 A 228 ASN HIS PRO ALA ALA ALA ILE ARG GLU ALA TYR ALA ALA SEQRES 4 A 228 GLY GLN ARG HIS PHE GLY GLU ASN ARG VAL GLN GLU ALA SEQRES 5 A 228 ILE ALA LYS GLN ALA GLU LEU THR ASP LEU PRO ASP LEU SEQRES 6 A 228 THR TRP HIS LEU LEU GLY LYS LEU GLN SER ASN LYS ALA SEQRES 7 A 228 ARG LYS ALA VAL GLU HIS PHE ASP TRP ILE HIS SER VAL SEQRES 8 A 228 ASP SER TRP ALA LEU ALA GLU ARG LEU ASP ARG ILE ALA SEQRES 9 A 228 GLY GLU LEU GLY ARG SER PRO LYS LEU CYS LEU GLN VAL SEQRES 10 A 228 LYS LEU LEU PRO ASP PRO ASN LYS ALA GLY TRP ASP PRO SEQRES 11 A 228 ALA ASP LEU ARG ALA GLU LEU PRO GLN LEU SER GLN LEU SEQRES 12 A 228 GLN GLN VAL GLN ILE ARG GLY LEU MET VAL ILE ALA PRO SEQRES 13 A 228 LEU GLY LEU THR ALA ALA GLU THR GLN ALA LEU PHE ALA SEQRES 14 A 228 GLN ALA ARG THR PHE ALA ALA GLU LEU GLN GLN GLN ALA SEQRES 15 A 228 PRO GLN LEU ARG LEU THR GLU LEU SER MET GLY MET SER SEQRES 16 A 228 SER ASP TRP PRO LEU ALA VAL ALA GLU GLY ALA THR TRP SEQRES 17 A 228 ILE ARG VAL GLY THR GLN LEU PHE GLY PRO ARG SER LEU SEQRES 18 A 228 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 228 MET ALA GLN ILE ALA GLU ARG LEU ALA SER LEU ARG SER SEQRES 2 B 228 GLN LEU PRO PRO SER VAL GLN LEU ILE ALA VAL SER LYS SEQRES 3 B 228 ASN HIS PRO ALA ALA ALA ILE ARG GLU ALA TYR ALA ALA SEQRES 4 B 228 GLY GLN ARG HIS PHE GLY GLU ASN ARG VAL GLN GLU ALA SEQRES 5 B 228 ILE ALA LYS GLN ALA GLU LEU THR ASP LEU PRO ASP LEU SEQRES 6 B 228 THR TRP HIS LEU LEU GLY LYS LEU GLN SER ASN LYS ALA SEQRES 7 B 228 ARG LYS ALA VAL GLU HIS PHE ASP TRP ILE HIS SER VAL SEQRES 8 B 228 ASP SER TRP ALA LEU ALA GLU ARG LEU ASP ARG ILE ALA SEQRES 9 B 228 GLY GLU LEU GLY ARG SER PRO LYS LEU CYS LEU GLN VAL SEQRES 10 B 228 LYS LEU LEU PRO ASP PRO ASN LYS ALA GLY TRP ASP PRO SEQRES 11 B 228 ALA ASP LEU ARG ALA GLU LEU PRO GLN LEU SER GLN LEU SEQRES 12 B 228 GLN GLN VAL GLN ILE ARG GLY LEU MET VAL ILE ALA PRO SEQRES 13 B 228 LEU GLY LEU THR ALA ALA GLU THR GLN ALA LEU PHE ALA SEQRES 14 B 228 GLN ALA ARG THR PHE ALA ALA GLU LEU GLN GLN GLN ALA SEQRES 15 B 228 PRO GLN LEU ARG LEU THR GLU LEU SER MET GLY MET SER SEQRES 16 B 228 SER ASP TRP PRO LEU ALA VAL ALA GLU GLY ALA THR TRP SEQRES 17 B 228 ILE ARG VAL GLY THR GLN LEU PHE GLY PRO ARG SER LEU SEQRES 18 B 228 GLU HIS HIS HIS HIS HIS HIS HET PLP A 301 15 HET PLP B 301 15 HET CA B 302 1 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM CA CALCIUM ION HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 5 CA CA 2+ FORMUL 6 HOH *162(H2 O) HELIX 1 AA1 GLN A 3 LEU A 15 1 13 HELIX 2 AA2 PRO A 29 ALA A 39 1 11 HELIX 3 AA3 ARG A 48 LEU A 59 1 12 HELIX 4 AA4 GLN A 74 ASN A 76 5 3 HELIX 5 AA5 LYS A 77 PHE A 85 1 9 HELIX 6 AA6 SER A 93 GLY A 108 1 16 HELIX 7 AA7 ASP A 129 GLN A 142 1 14 HELIX 8 AA8 THR A 160 ALA A 182 1 23 HELIX 9 AA9 ASP A 197 GLU A 204 1 8 HELIX 10 AB1 GLY A 212 GLY A 217 1 6 HELIX 11 AB2 ILE B 4 LEU B 15 1 12 HELIX 12 AB3 PRO B 29 ALA B 39 1 11 HELIX 13 AB4 ARG B 48 GLU B 58 1 11 HELIX 14 AB5 LYS B 77 PHE B 85 1 9 HELIX 15 AB6 SER B 93 GLY B 108 1 16 HELIX 16 AB7 ASP B 129 GLU B 136 1 8 HELIX 17 AB8 GLU B 136 LEU B 143 1 8 HELIX 18 AB9 THR B 160 ALA B 182 1 23 HELIX 19 AC1 ASP B 197 GLU B 204 1 8 HELIX 20 AC2 GLY B 212 GLY B 217 1 6 SHEET 1 AA1 9 GLN A 20 VAL A 24 0 SHEET 2 AA1 9 HIS A 43 GLU A 46 1 O GLY A 45 N ALA A 23 SHEET 3 AA1 9 THR A 66 LEU A 69 1 O HIS A 68 N PHE A 44 SHEET 4 AA1 9 TRP A 87 VAL A 91 1 O HIS A 89 N LEU A 69 SHEET 5 AA1 9 LYS A 112 GLN A 116 1 O LYS A 112 N ILE A 88 SHEET 6 AA1 9 GLN A 147 MET A 152 1 O GLN A 147 N LEU A 113 SHEET 7 AA1 9 GLU A 189 SER A 191 1 O SER A 191 N LEU A 151 SHEET 8 AA1 9 TRP A 208 VAL A 211 1 N TRP A 208 O LEU A 190 SHEET 9 AA1 9 GLN A 20 VAL A 24 1 N ILE A 22 O ILE A 209 SHEET 1 AA2 9 GLN B 20 VAL B 24 0 SHEET 2 AA2 9 HIS B 43 GLU B 46 1 O GLY B 45 N ALA B 23 SHEET 3 AA2 9 THR B 66 LEU B 69 1 O HIS B 68 N PHE B 44 SHEET 4 AA2 9 TRP B 87 VAL B 91 1 O TRP B 87 N LEU B 69 SHEET 5 AA2 9 LYS B 112 GLN B 116 1 O LYS B 112 N ILE B 88 SHEET 6 AA2 9 GLN B 147 MET B 152 1 O GLN B 147 N LEU B 113 SHEET 7 AA2 9 GLU B 189 SER B 191 1 O SER B 191 N LEU B 151 SHEET 8 AA2 9 TRP B 208 VAL B 211 1 N TRP B 208 O LEU B 190 SHEET 9 AA2 9 GLN B 20 VAL B 24 1 N VAL B 24 O VAL B 211 LINK NZ LYS A 26 C4A PLP A 301 1555 1555 1.27 LINK NZ LYS B 26 C4A PLP B 301 1555 1555 1.25 LINK O HOH A 469 CA CA B 302 2455 1555 2.35 LINK O HOH A 491 CA CA B 302 2455 1555 2.40 LINK O PRO B 63 CA CA B 302 1555 1555 2.42 LINK CA CA B 302 O HOH B 408 1555 1555 2.50 LINK CA CA B 302 O HOH B 429 1555 1555 2.37 LINK CA CA B 302 O HOH B 433 1555 1555 2.47 LINK CA CA B 302 O HOH B 452 1555 1555 2.30 SITE 1 AC1 12 VAL A 24 LYS A 26 ASN A 47 LEU A 70 SITE 2 AC1 12 MET A 152 MET A 194 SER A 195 ARG A 210 SITE 3 AC1 12 GLY A 212 THR A 213 HOH A 418 HOH A 428 SITE 1 AC2 7 HOH A 469 HOH A 491 PRO B 63 HOH B 408 SITE 2 AC2 7 HOH B 429 HOH B 433 HOH B 452 SITE 1 AC3 17 VAL B 24 SER B 25 ASN B 27 HIS B 28 SITE 2 AC3 17 GLY B 45 GLU B 46 ASN B 47 GLU B 51 SITE 3 AC3 17 LEU B 70 MET B 194 SER B 195 ARG B 210 SITE 4 AC3 17 VAL B 211 GLY B 212 THR B 213 HOH B 413 SITE 5 AC3 17 HOH B 427 CRYST1 46.627 98.937 103.737 90.00 90.00 90.00 P 21 21 21 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 0.021447 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010107 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009640 0.00000