HEADER TRANSFERASE 12-MAY-23 8SUJ TITLE JOINT X-RAY/NEUTRON STRUCTURE OF THERMUS THERMOPHILUS SERINE TITLE 2 HYDROXYMETHYLTRANSFERASE (TTHSHMT) IN INTERNAL ALDIMINE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE HYDROXYMETHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SHMT,SERINE METHYLASE; COMPND 5 EC: 2.1.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS HB8; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 GENE: GLYA, TTHA1524; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PYRIDOXAL 5'-PHOSPHATE, PLP, FOLD TYPE 1, ONE CARBON METABOLISM, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION AUTHOR V.N.DRAGO,A.KOVALEVSKY REVDAT 2 15-NOV-23 8SUJ 1 REMARK REVDAT 1 16-AUG-23 8SUJ 0 JRNL AUTH V.N.DRAGO,C.CAMPOS,M.HOOPER,A.COLLINS,O.GERLITS,K.L.WEISS, JRNL AUTH 2 M.P.BLAKELEY,R.S.PHILLIPS,A.KOVALEVSKY JRNL TITL REVEALING PROTONATION STATES AND TRACKING SUBSTRATE IN JRNL TITL 2 SERINE HYDROXYMETHYLTRANSFERASE WITH ROOM-TEMPERATURE X-RAY JRNL TITL 3 AND NEUTRON CRYSTALLOGRAPHY. JRNL REF COMMUN CHEM V. 6 162 2023 JRNL REFN ESSN 2399-3669 JRNL PMID 37532884 JRNL DOI 10.1038/S42004-023-00964-9 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.D.ADAMS,M.MUSTYAKIMOV,P.V.AFONINE,P.LANGAN REMARK 1 TITL GENERALIZED X-RAY AND NEUTRON CRYSTALLOGRAPHIC ANALYSIS: REMARK 1 TITL 2 MORE ACCURATE AND COMPLETE STRUCTURES FOR BIOLOGICAL REMARK 1 TITL 3 MACROMOLECULES REMARK 1 REF ACTA CRYST. V. D65 567 2009 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NCNS 1.0.8 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN,MUSTYAKIMOV, REMARK 3 : AFONINE,LANGAN REMARK 3 NEUTRON DATA. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 75.5 REMARK 3 NUMBER OF REFLECTIONS : 31065 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1553 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 64.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3150 REMARK 3 BIN R VALUE (WORKING SET) : 0.3620 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 173 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.35 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.46 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 3 X-RAY DATA. REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.500 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 58902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2954 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6235 REMARK 3 BIN R VALUE (WORKING SET) : 0.1940 REMARK 3 BIN FREE R VALUE : 0.1930 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 291 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.35 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8SUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274495. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 5.5 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 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NONE REMARK 200 OPTICS : OSMIC VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62364 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 95.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.36400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 230 REMARK 230 EXPERIMENTAL DETAILS REMARK 230 EXPERIMENT TYPE : NEUTRON DIFFRACTION REMARK 230 DATE OF DATA COLLECTION : 29-MAR-22 REMARK 230 TEMPERATURE (KELVIN) : 293.0 REMARK 230 PH : 5.50 REMARK 230 NUMBER OF CRYSTALS USED : NULL REMARK 230 REMARK 230 NEUTRON SOURCE : NUCLEAR REACTOR REMARK 230 BEAMLINE : CG4D REMARK 230 WAVELENGTH OR RANGE (A) : 2.8-4.5 REMARK 230 MONOCHROMATOR : NONE REMARK 230 OPTICS : ELLIPTICAL MIRRORS REMARK 230 REMARK 230 DETECTOR TYPE : IMAGE PLATE REMARK 230 DETECTOR MANUFACTURER : MAATEL IMAGINE REMARK 230 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO, LAUEGEN REMARK 230 DATA SCALING SOFTWARE : CRYSALISPRO, SCALA REMARK 230 REMARK 230 NUMBER OF UNIQUE REFLECTIONS : 32586 REMARK 230 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 230 RESOLUTION RANGE LOW (A) : 47.780 REMARK 230 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 230 REMARK 230 OVERALL. REMARK 230 COMPLETENESS FOR RANGE (%) : 85.4 REMARK 230 DATA REDUNDANCY : 4.100 REMARK 230 R MERGE (I) : 0.16100 REMARK 230 R SYM (I) : NULL REMARK 230 FOR THE DATA SET : 4.3000 REMARK 230 REMARK 230 IN THE HIGHEST RESOLUTION SHELL. REMARK 230 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 230 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 230 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 230 DATA REDUNDANCY IN SHELL : 3.80 REMARK 230 R MERGE FOR SHELL (I) : 0.28100 REMARK 230 R SYM FOR SHELL (I) : NULL REMARK 230 FOR SHELL : 2.900 REMARK 230 REMARK 230 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 230 SOFTWARE USED : PHASER REMARK 230 STARTING MODEL: NULL REMARK 230 REMARK 230 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MM NAOAC PH 5.5, 1.0 M (NH4)2SO4, REMARK 280 AND 0.5 M LI2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 41.66700 REMARK 290 SMTRY3 2 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: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -96.0 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 SER A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 REMARK 465 SER B 1003 REMARK 465 THR B 1004 REMARK 465 LEU B 1005 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 ASN A 49 D2 DOD A 2102 1.41 REMARK 500 O DOD A 2123 D2 DOD A 2305 1.48 REMARK 500 OG SER A 355 D2 DOD A 2104 1.51 REMARK 500 DH TYR A 216 O DOD A 2103 1.52 REMARK 500 HH TYR A 216 O DOD A 2103 1.52 REMARK 500 D1 DOD B 1734 O DOD B 1739 1.53 REMARK 500 OD1 ASN B 1098 DG1 THR B 1221 1.53 REMARK 500 O DOD B 1727 D1 DOD B 1797 1.54 REMARK 500 O VAL B 1353 DG1 THR B 1354 1.55 REMARK 500 O VAL B 1353 HG1 THR B 1354 1.55 REMARK 500 O VAL A 305 DG1 THR A 306 1.55 REMARK 500 O VAL A 305 HG1 THR A 306 1.55 REMARK 500 O DOD A 2303 D1 DOD B 1791 1.56 REMARK 500 O PRO A 108 D2 DOD A 2106 1.57 REMARK 500 O DOD B 1644 D2 DOD B 1784 1.58 REMARK 500 D1 DOD A 2212 O DOD A 2223 1.58 REMARK 500 O DOD A 2157 D1 DOD B 1746 1.59 REMARK 500 O GLY A 142 D2 DOD A 2109 1.60 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 LLP A 226 -133.15 82.74 REMARK 500 THR A 306 -0.09 71.43 REMARK 500 ASN A 311 -146.66 -127.29 REMARK 500 THR A 354 167.52 60.38 REMARK 500 ALA B1058 58.63 -143.60 REMARK 500 ALA B1173 38.47 -144.23 REMARK 500 LLP B1226 -131.77 84.60 REMARK 500 SER B1238 147.24 -172.89 REMARK 500 ASN B1311 -149.37 -130.25 REMARK 500 THR B1354 167.53 59.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG B1040 0.08 SIDE CHAIN REMARK 500 ARG B1156 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8SUJ A 3 407 UNP Q5SI56 GLYA_THET8 3 407 DBREF 8SUJ B 1003 1407 UNP Q5SI56 GLYA_THET8 3 407 SEQRES 1 A 405 SER THR LEU LYS ARG ASP GLU ALA LEU PHE GLU LEU ILE SEQRES 2 A 405 ALA LEU GLU GLU LYS ARG GLN ARG GLU GLY LEU GLU LEU SEQRES 3 A 405 ILE ALA SER GLU ASN PHE VAL SER LYS GLN VAL ARG GLU SEQRES 4 A 405 ALA VAL GLY SER VAL LEU THR ASN LYS TYR ALA GLU GLY SEQRES 5 A 405 TYR PRO GLY ALA ARG TYR TYR GLY GLY CYS GLU VAL ILE SEQRES 6 A 405 ASP ARG VAL GLU SER LEU ALA ILE GLU ARG ALA LYS ALA SEQRES 7 A 405 LEU PHE GLY ALA ALA TRP ALA ASN VAL GLN PRO HIS SER SEQRES 8 A 405 GLY SER GLN ALA ASN MET ALA VAL TYR MET ALA LEU MET SEQRES 9 A 405 GLU PRO GLY ASP THR LEU MET GLY MET ASP LEU ALA ALA SEQRES 10 A 405 GLY GLY HIS LEU THR HIS GLY SER ARG VAL ASN PHE SER SEQRES 11 A 405 GLY LYS LEU TYR LYS VAL VAL SER TYR GLY VAL ARG PRO SEQRES 12 A 405 ASP THR GLU LEU ILE ASP LEU GLU GLU VAL ARG ARG LEU SEQRES 13 A 405 ALA LEU GLU HIS ARG PRO LYS VAL ILE VAL ALA GLY ALA SEQRES 14 A 405 SER ALA TYR PRO ARG PHE TRP ASP PHE LYS ALA PHE ARG SEQRES 15 A 405 GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU VAL VAL ASP SEQRES 16 A 405 MET ALA HIS PHE ALA GLY LEU VAL ALA ALA GLY LEU HIS SEQRES 17 A 405 PRO ASN PRO LEU PRO TYR ALA HIS VAL VAL THR SER THR SEQRES 18 A 405 THR HIS LLP THR LEU ARG GLY PRO ARG GLY GLY LEU ILE SEQRES 19 A 405 LEU SER ASN ASP PRO GLU LEU GLY LYS ARG ILE ASP LYS SEQRES 20 A 405 LEU ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU GLU HIS SEQRES 21 A 405 VAL ILE ALA GLY LYS ALA VAL ALA PHE PHE GLU ALA LEU SEQRES 22 A 405 GLN PRO GLU PHE LYS GLU TYR SER ARG LEU VAL VAL GLU SEQRES 23 A 405 ASN ALA LYS ARG LEU ALA GLU GLU LEU ALA ARG ARG GLY SEQRES 24 A 405 TYR ARG ILE VAL THR GLY GLY THR ASP ASN HIS LEU PHE SEQRES 25 A 405 LEU VAL ASP LEU ARG PRO LYS GLY LEU THR GLY LYS GLU SEQRES 26 A 405 ALA GLU GLU ARG LEU ASP ALA VAL GLY ILE THR VAL ASN SEQRES 27 A 405 LYS ASN ALA ILE PRO PHE ASP PRO LYS PRO PRO ARG VAL SEQRES 28 A 405 THR SER GLY ILE ARG ILE GLY THR PRO ALA ILE THR THR SEQRES 29 A 405 ARG GLY PHE THR PRO GLU GLU MET PRO LEU VAL ALA GLU SEQRES 30 A 405 LEU ILE ASP ARG ALA LEU LEU GLU GLY PRO SER GLU ALA SEQRES 31 A 405 LEU ARG GLU GLU VAL ARG ARG LEU ALA LEU ALA HIS PRO SEQRES 32 A 405 MET PRO SEQRES 1 B 405 SER THR LEU LYS ARG ASP GLU ALA LEU PHE GLU LEU ILE SEQRES 2 B 405 ALA LEU GLU GLU LYS ARG GLN ARG GLU GLY LEU GLU LEU SEQRES 3 B 405 ILE ALA SER GLU ASN PHE VAL SER LYS GLN VAL ARG GLU SEQRES 4 B 405 ALA VAL GLY SER VAL LEU THR ASN LYS TYR ALA GLU GLY SEQRES 5 B 405 TYR PRO GLY ALA ARG TYR TYR GLY GLY CYS GLU VAL ILE SEQRES 6 B 405 ASP ARG VAL GLU SER LEU ALA ILE GLU ARG ALA LYS ALA SEQRES 7 B 405 LEU PHE GLY ALA ALA TRP ALA ASN VAL GLN PRO HIS SER SEQRES 8 B 405 GLY SER GLN ALA ASN MET ALA VAL TYR MET ALA LEU MET SEQRES 9 B 405 GLU PRO GLY ASP THR LEU MET GLY MET ASP LEU ALA ALA SEQRES 10 B 405 GLY GLY HIS LEU THR HIS GLY SER ARG VAL ASN PHE SER SEQRES 11 B 405 GLY LYS LEU TYR LYS VAL VAL SER TYR GLY VAL ARG PRO SEQRES 12 B 405 ASP THR GLU LEU ILE ASP LEU GLU GLU VAL ARG ARG LEU SEQRES 13 B 405 ALA LEU GLU HIS ARG PRO LYS VAL ILE VAL ALA GLY ALA SEQRES 14 B 405 SER ALA TYR PRO ARG PHE TRP ASP PHE LYS ALA PHE ARG SEQRES 15 B 405 GLU ILE ALA ASP GLU VAL GLY ALA TYR LEU VAL VAL ASP SEQRES 16 B 405 MET ALA HIS PHE ALA GLY LEU VAL ALA ALA GLY LEU HIS SEQRES 17 B 405 PRO ASN PRO LEU PRO TYR ALA HIS VAL VAL THR SER THR SEQRES 18 B 405 THR HIS LLP THR LEU ARG GLY PRO ARG GLY GLY LEU ILE SEQRES 19 B 405 LEU SER ASN ASP PRO GLU LEU GLY LYS ARG ILE ASP LYS SEQRES 20 B 405 LEU ILE PHE PRO GLY ILE GLN GLY GLY PRO LEU GLU HIS SEQRES 21 B 405 VAL ILE ALA GLY LYS ALA VAL ALA PHE PHE GLU ALA LEU SEQRES 22 B 405 GLN PRO GLU PHE LYS GLU TYR SER ARG LEU VAL VAL GLU SEQRES 23 B 405 ASN ALA LYS ARG LEU ALA GLU GLU LEU ALA ARG ARG GLY SEQRES 24 B 405 TYR ARG ILE VAL THR GLY GLY THR ASP ASN HIS LEU PHE SEQRES 25 B 405 LEU VAL ASP LEU ARG PRO LYS GLY LEU THR GLY LYS GLU SEQRES 26 B 405 ALA GLU GLU ARG LEU ASP ALA VAL GLY ILE THR VAL ASN SEQRES 27 B 405 LYS ASN ALA ILE PRO PHE ASP PRO LYS PRO PRO ARG VAL SEQRES 28 B 405 THR SER GLY ILE ARG ILE GLY THR PRO ALA ILE THR THR SEQRES 29 B 405 ARG GLY PHE THR PRO GLU GLU MET PRO LEU VAL ALA GLU SEQRES 30 B 405 LEU ILE ASP ARG ALA LEU LEU GLU GLY PRO SER GLU ALA SEQRES 31 B 405 LEU ARG GLU GLU VAL ARG ARG LEU ALA LEU ALA HIS PRO SEQRES 32 B 405 MET PRO MODRES 8SUJ LLP A 226 LYS MODIFIED RESIDUE MODRES 8SUJ LLP B 1226 LYS MODIFIED RESIDUE HET LLP A 226 42 HET LLP B1226 42 HET SO4 A2001 5 HET SO4 B1501 5 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM SO4 SULFATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 DOD *429(D2 O) HELIX 1 AA1 ASP A 8 GLU A 24 1 17 HELIX 2 AA2 SER A 36 GLY A 44 1 9 HELIX 3 AA3 SER A 45 LYS A 50 5 6 HELIX 4 AA4 CYS A 64 GLY A 83 1 20 HELIX 5 AA5 SER A 93 MET A 106 1 14 HELIX 6 AA6 LEU A 117 GLY A 120 5 4 HELIX 7 AA7 HIS A 122 GLY A 126 5 5 HELIX 8 AA8 ASN A 130 TYR A 136 1 7 HELIX 9 AA9 ASP A 151 ARG A 163 1 13 HELIX 10 AB1 ASP A 179 GLY A 191 1 13 HELIX 11 AB2 PHE A 201 ALA A 207 1 7 HELIX 12 AB3 HIS A 225 ARG A 229 5 5 HELIX 13 AB4 ASP A 240 PHE A 252 1 13 HELIX 14 AB5 LEU A 260 LEU A 275 1 16 HELIX 15 AB6 GLN A 276 ARG A 300 1 25 HELIX 16 AB7 THR A 306 GLY A 308 5 3 HELIX 17 AB8 ARG A 319 GLY A 322 5 4 HELIX 18 AB9 THR A 324 ALA A 334 1 11 HELIX 19 AC1 THR A 361 ARG A 367 1 7 HELIX 20 AC2 THR A 370 GLU A 372 5 3 HELIX 21 AC3 GLU A 373 GLY A 388 1 16 HELIX 22 AC4 SER A 390 ALA A 403 1 14 HELIX 23 AC5 ASP B 1008 GLY B 1025 1 18 HELIX 24 AC6 SER B 1036 GLY B 1044 1 9 HELIX 25 AC7 SER B 1045 LYS B 1050 5 6 HELIX 26 AC8 CYS B 1064 GLY B 1083 1 20 HELIX 27 AC9 SER B 1093 MET B 1106 1 14 HELIX 28 AD1 HIS B 1122 GLY B 1126 5 5 HELIX 29 AD2 ASN B 1130 TYR B 1136 1 7 HELIX 30 AD3 ASP B 1151 ARG B 1163 1 13 HELIX 31 AD4 ASP B 1179 VAL B 1190 1 12 HELIX 32 AD5 PHE B 1201 ALA B 1207 1 7 HELIX 33 AD6 HIS B 1225 ARG B 1229 5 5 HELIX 34 AD7 ASP B 1240 PHE B 1252 1 13 HELIX 35 AD8 LEU B 1260 LEU B 1275 1 16 HELIX 36 AD9 GLN B 1276 ARG B 1299 1 24 HELIX 37 AE1 THR B 1306 GLY B 1308 5 3 HELIX 38 AE2 ARG B 1319 GLY B 1322 5 4 HELIX 39 AE3 THR B 1324 VAL B 1335 1 12 HELIX 40 AE4 THR B 1361 ARG B 1367 1 7 HELIX 41 AE5 THR B 1370 GLU B 1372 5 3 HELIX 42 AE6 GLU B 1373 GLU B 1387 1 15 HELIX 43 AE7 SER B 1390 ALA B 1403 1 14 SHEET 1 AA1 2 LEU A 26 GLU A 27 0 SHEET 2 AA1 2 ILE A 337 THR A 338 1 O THR A 338 N LEU A 26 SHEET 1 AA2 2 GLY A 54 TYR A 55 0 SHEET 2 AA2 2 ALA A 58 ARG A 59 -1 O ALA A 58 N TYR A 55 SHEET 1 AA3 7 TRP A 86 ASN A 88 0 SHEET 2 AA3 7 GLY A 234 SER A 238 -1 O ILE A 236 N ASN A 88 SHEET 3 AA3 7 VAL A 219 THR A 223 -1 N VAL A 220 O LEU A 237 SHEET 4 AA3 7 TYR A 193 ASP A 197 1 N VAL A 196 O THR A 221 SHEET 5 AA3 7 VAL A 166 ALA A 169 1 N ILE A 167 O VAL A 195 SHEET 6 AA3 7 THR A 111 MET A 115 1 N MET A 113 O VAL A 168 SHEET 7 AA3 7 LYS A 137 TYR A 141 1 O LYS A 137 N LEU A 112 SHEET 1 AA4 4 ARG A 303 ILE A 304 0 SHEET 2 AA4 4 LEU A 313 ASP A 317 -1 O ASP A 317 N ARG A 303 SHEET 3 AA4 4 GLY A 356 GLY A 360 -1 O ILE A 357 N VAL A 316 SHEET 4 AA4 4 ASN A 340 LYS A 341 -1 N ASN A 340 O ARG A 358 SHEET 1 AA5 2 LEU B1026 GLU B1027 0 SHEET 2 AA5 2 ILE B1337 THR B1338 1 O THR B1338 N LEU B1026 SHEET 1 AA6 2 GLY B1054 TYR B1055 0 SHEET 2 AA6 2 ALA B1058 ARG B1059 -1 O ALA B1058 N TYR B1055 SHEET 1 AA7 7 TRP B1086 ASN B1088 0 SHEET 2 AA7 7 GLY B1234 SER B1238 -1 O ILE B1236 N ASN B1088 SHEET 3 AA7 7 VAL B1219 THR B1223 -1 N VAL B1220 O LEU B1237 SHEET 4 AA7 7 TYR B1193 ASP B1197 1 N VAL B1196 O VAL B1219 SHEET 5 AA7 7 VAL B1166 ALA B1169 1 N ILE B1167 O VAL B1195 SHEET 6 AA7 7 THR B1111 MET B1115 1 N MET B1113 O VAL B1168 SHEET 7 AA7 7 LYS B1137 TYR B1141 1 O LYS B1137 N LEU B1112 SHEET 1 AA8 4 ARG B1303 ILE B1304 0 SHEET 2 AA8 4 LEU B1313 ASP B1317 -1 O ASP B1317 N ARG B1303 SHEET 3 AA8 4 GLY B1356 GLY B1360 -1 O ILE B1359 N PHE B1314 SHEET 4 AA8 4 ASN B1340 ASN B1342 -1 N ASN B1342 O GLY B1356 LINK C HIS A 225 N LLP A 226 1555 1555 1.33 LINK C LLP A 226 N THR A 227 1555 1555 1.34 LINK C HIS B1225 N LLP B1226 1555 1555 1.32 LINK C LLP B1226 N THR B1227 1555 1555 1.34 CISPEP 1 PHE A 252 PRO A 253 0 0.58 CISPEP 2 PHE B 1252 PRO B 1253 0 1.17 CRYST1 58.807 83.334 95.568 90.00 91.68 90.00 P 1 21 1 4 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 0.017005 0.000000 0.000499 0.00000 SCALE2 0.000000 0.012000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010468 0.00000