HEADER ISOMERASE 02-JUL-19 6PNL TITLE STRUCTURE OF EPIMERASE MTH375 FROM THE THERMOPHILIC PSEUDOMUREIN- TITLE 2 CONTAINING METHANOGEN METHANOTHERMOBACTER THERMAUTOTROPHICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-GLUCOSE 4-EPIMERASE RELATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 145262; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PSEUDOMUREIN, UDP-N-ACETYLGLUCOSAMINE, EPIMERASE, CELL WALL, KEYWDS 2 METHANOTHERMOBACTER, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CARBONE,L.R.SCHOFIELD,A.J.SUTHERLAND-SMITH,R.S.RONIMUS REVDAT 4 27-DEC-23 6PNL 1 TITLE COMPND REVDAT 3 11-OCT-23 6PNL 1 REMARK REVDAT 2 09-AUG-23 6PNL 1 SOURCE REVDAT 1 08-JUL-20 6PNL 0 JRNL AUTH V.CARBONE,L.R.SCHOFIELD,A.J.SUTHERLAND-SMITH,R.S.RONIMUS JRNL TITL STRUCTURE OF A UDP-GALE 4-EPIMERASE (MTH375) FROM THE JRNL TITL 2 THERMOPHILIC PSEUDOMUREIN-CONTAINING METHANOGEN JRNL TITL 3 METHANOTHERMOBACTER THERMAUTOTROPHICUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.01 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26639 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1379 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1902 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : 0.24000 REMARK 3 B33 (A**2) : -0.79000 REMARK 3 B12 (A**2) : 0.12000 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): 0.155 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.015 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2944 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2710 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4008 ; 1.399 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6225 ; 0.954 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 350 ; 6.120 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;35.433 ;23.758 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 470 ;14.739 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;18.709 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 422 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3346 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 718 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 6PNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1000242768. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-17 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.953653 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.3 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28060 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 46.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.19200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 18.70 REMARK 200 R MERGE FOR SHELL (I) : 0.98700 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: 6PMH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CHLORIDE, 1.6 M AMMONIUM REMARK 280 SULFATE 0.1 M SODIUM HEPES, 3.0% W/V 1,8-DIAMINOOCTANE, PH 7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K 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 87.34750 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 87.34750 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 87.34750 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 87.34750 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 87.34750 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 87.34750 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: 8170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 87.34750 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 676 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -35 REMARK 465 ARG A -34 REMARK 465 GLY A -33 REMARK 465 SER A -32 REMARK 465 HIS A -31 REMARK 465 HIS A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 GLY A -25 REMARK 465 MET A -24 REMARK 465 ALA A -23 REMARK 465 SER A -22 REMARK 465 MET A -21 REMARK 465 THR A -20 REMARK 465 GLY A -19 REMARK 465 GLY A -18 REMARK 465 GLN A -17 REMARK 465 GLN A -16 REMARK 465 MET A -15 REMARK 465 GLY A -14 REMARK 465 ARG A -13 REMARK 465 ASP A -12 REMARK 465 LEU A -11 REMARK 465 TYR A -10 REMARK 465 ASP A -9 REMARK 465 ASP A -8 REMARK 465 ASP A -7 REMARK 465 ASP A -6 REMARK 465 LYS A -5 REMARK 465 ASP A -4 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 PRO A 141 C - N - CD ANGL. DEV. = 14.5 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 SER A 46 45.47 -143.75 REMARK 500 ALA A 90 -112.12 -139.64 REMARK 500 ASP A 146 53.17 -98.27 REMARK 500 ASN A 184 73.42 23.32 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 NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6PMH RELATED DB: PDB REMARK 900 CONTAINS THE SAME PROTEIN COMPLEXED WITH AMP AND UDP DBREF 6PNL A 1 332 UNP O26475 O26475_METTH 1 332 SEQADV 6PNL MET A -35 UNP O26475 INITIATING METHIONINE SEQADV 6PNL ARG A -34 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLY A -33 UNP O26475 EXPRESSION TAG SEQADV 6PNL SER A -32 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -31 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -30 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -29 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -28 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -27 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -26 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLY A -25 UNP O26475 EXPRESSION TAG SEQADV 6PNL MET A -24 UNP O26475 EXPRESSION TAG SEQADV 6PNL ALA A -23 UNP O26475 EXPRESSION TAG SEQADV 6PNL SER A -22 UNP O26475 EXPRESSION TAG SEQADV 6PNL MET A -21 UNP O26475 EXPRESSION TAG SEQADV 6PNL THR A -20 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLY A -19 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLY A -18 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLN A -17 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLN A -16 UNP O26475 EXPRESSION TAG SEQADV 6PNL MET A -15 UNP O26475 EXPRESSION TAG SEQADV 6PNL GLY A -14 UNP O26475 EXPRESSION TAG SEQADV 6PNL ARG A -13 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -12 UNP O26475 EXPRESSION TAG SEQADV 6PNL LEU A -11 UNP O26475 EXPRESSION TAG SEQADV 6PNL TYR A -10 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -9 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -8 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -7 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -6 UNP O26475 EXPRESSION TAG SEQADV 6PNL LYS A -5 UNP O26475 EXPRESSION TAG SEQADV 6PNL ASP A -4 UNP O26475 EXPRESSION TAG SEQADV 6PNL HIS A -3 UNP O26475 EXPRESSION TAG SEQADV 6PNL PRO A -2 UNP O26475 EXPRESSION TAG SEQADV 6PNL PHE A -1 UNP O26475 EXPRESSION TAG SEQADV 6PNL THR A 0 UNP O26475 EXPRESSION TAG SEQRES 1 A 368 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA SEQRES 2 A 368 SER MET THR GLY GLY GLN GLN MET GLY ARG ASP LEU TYR SEQRES 3 A 368 ASP ASP ASP ASP LYS ASP HIS PRO PHE THR MET ILE MET SEQRES 4 A 368 ASP GLU PHE ARG ALA TYR ASP GLY LYS CME VAL LEU VAL SEQRES 5 A 368 THR GLY GLY ALA GLY CYS VAL GLY SER ASN LEU THR GLY SEQRES 6 A 368 ASN LEU ALA LYS ALA GLY ALA ASN VAL ILE ILE LEU ASP SEQRES 7 A 368 ASN LEU SER SER SER TYR GLU TRP ASN ILE PRO GLU TYR SEQRES 8 A 368 GLU ASN ILE GLU PHE VAL LYS GLY ASP ILE LEU ASP ASP SEQRES 9 A 368 GLU VAL LEU LYS ARG VAL PHE LYS GLU ARG PRO ASP TYR SEQRES 10 A 368 VAL PHE HIS LEU ALA ALA HIS PHE ALA ASN GLN ASN SER SEQRES 11 A 368 VAL ASP ASN PRO GLU LYS ASP LEU LEU VAL ASN GLY LEU SEQRES 12 A 368 GLY ILE LEU LYS VAL LEU GLU TYR ALA GLN LEU VAL GLY SEQRES 13 A 368 VAL GLU ARG PHE VAL TYR SER SER SER GLY CME GLY VAL SEQRES 14 A 368 TYR GLY LEU ASP SER LYS ILE PRO PHE GLU GLU HIS ASP SEQRES 15 A 368 ILE SER ILE SER LEU HIS THR PRO TYR GLN VAL THR LYS SEQRES 16 A 368 LEU LEU GLY GLU LEU TYR THR ASN TYR PHE HIS ASN LEU SEQRES 17 A 368 TYR GLU MET PRO ILE VAL ASN ALA ARG PHE PHE ASN VAL SEQRES 18 A 368 PHE GLY PRO GLY GLU VAL PRO GLY LYS TYR ARG ASN VAL SEQRES 19 A 368 ILE PRO ASN PHE PHE TYR TRP ALA MET ASN GLN GLN PRO SEQRES 20 A 368 LEU PRO ILE THR GLY ASP GLY SER GLU THR ARG ASP TRP SEQRES 21 A 368 THR PHE VAL GLU ASP ILE VAL ARG GLY LEU MET ALA MET SEQRES 22 A 368 GLY VAL ARG ARG GLU ALA ILE GLY GLU ALA ILE ASN LEU SEQRES 23 A 368 GLY SER GLY THR GLU HIS GLN VAL ILE GLU MET ALA GLY SEQRES 24 A 368 ILE ILE ASN GLU LEU THR GLU ASN PRO ALA GLY VAL VAL SEQRES 25 A 368 TYR ARG PRO ARG ARG ASP TRP ASP ALA LYS THR ARG LEU SEQRES 26 A 368 LEU SER SER ILE ASP LYS ALA ARG ARG LEU LEU ASP TYR SEQRES 27 A 368 GLU PRO GLN VAL SER PHE ARG GLU GLY LEU GLU ARG THR SEQRES 28 A 368 HIS ARG TRP PHE THR GLU ASN TRP GLU LEU ILE ARG LYS SEQRES 29 A 368 SER ALA GLU PHE MODRES 6PNL CME A 13 CYS MODIFIED RESIDUE MODRES 6PNL CME A 131 CYS MODIFIED RESIDUE HET CME A 13 10 HET CME A 131 10 HET NAD A 401 44 HET UDP A 402 25 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET SO4 A 406 5 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 2 NAD C21 H27 N7 O14 P2 FORMUL 3 UDP C9 H14 N2 O12 P2 FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *239(H2 O) HELIX 1 AA1 PHE A -1 PHE A 6 1 8 HELIX 2 AA2 ARG A 7 ASP A 10 5 4 HELIX 3 AA3 GLY A 21 ALA A 34 1 14 HELIX 4 AA4 TYR A 48 ILE A 52 5 5 HELIX 5 AA5 ASP A 67 LYS A 76 1 10 HELIX 6 AA6 ALA A 90 ASN A 97 1 8 HELIX 7 AA7 ASN A 97 GLY A 106 1 10 HELIX 8 AA8 GLY A 106 GLY A 120 1 15 HELIX 9 AA9 GLY A 130 TYR A 134 1 5 HELIX 10 AB1 THR A 153 GLU A 174 1 22 HELIX 11 AB2 ASN A 197 MET A 207 1 11 HELIX 12 AB3 VAL A 227 ARG A 240 1 14 HELIX 13 AB4 ARG A 241 ILE A 244 5 4 HELIX 14 AB5 VAL A 258 THR A 269 1 12 HELIX 15 AB6 ILE A 293 ASP A 301 1 9 HELIX 16 AB7 SER A 307 ASN A 322 1 16 HELIX 17 AB8 ASN A 322 ALA A 330 1 9 SHEET 1 AA1 7 ILE A 58 LYS A 62 0 SHEET 2 AA1 7 ASN A 37 ASP A 42 1 N ILE A 40 O VAL A 61 SHEET 3 AA1 7 CME A 13 THR A 17 1 N VAL A 16 O ILE A 39 SHEET 4 AA1 7 TYR A 81 HIS A 84 1 O TYR A 81 N LEU A 15 SHEET 5 AA1 7 ARG A 123 SER A 129 1 O VAL A 125 N VAL A 82 SHEET 6 AA1 7 ILE A 177 PHE A 182 1 O VAL A 178 N TYR A 126 SHEET 7 AA1 7 ALA A 247 LEU A 250 1 O LEU A 250 N ARG A 181 SHEET 1 AA2 2 VAL A 185 PHE A 186 0 SHEET 2 AA2 2 THR A 225 PHE A 226 1 O THR A 225 N PHE A 186 SHEET 1 AA3 2 LEU A 212 THR A 215 0 SHEET 2 AA3 2 VAL A 275 ARG A 278 1 O VAL A 276 N ILE A 214 SHEET 1 AA4 2 THR A 221 ARG A 222 0 SHEET 2 AA4 2 HIS A 256 GLN A 257 -1 O HIS A 256 N ARG A 222 LINK C LYS A 12 N CME A 13 1555 1555 1.33 LINK C CME A 13 N VAL A 14 1555 1555 1.33 LINK C GLY A 130 N CME A 131 1555 1555 1.33 LINK C CME A 131 N GLY A 132 1555 1555 1.33 CISPEP 1 PHE A 89 ALA A 90 0 -10.56 CISPEP 2 ILE A 140 PRO A 141 0 -0.03 SITE 1 AC1 34 GLY A 18 GLY A 21 CYS A 22 VAL A 23 SITE 2 AC1 34 ASP A 42 ASN A 43 LEU A 44 SER A 45 SITE 3 AC1 34 SER A 46 SER A 47 GLY A 63 ASP A 64 SITE 4 AC1 34 ILE A 65 LEU A 85 ALA A 86 ALA A 87 SITE 5 AC1 34 VAL A 104 SER A 127 SER A 128 SER A 129 SITE 6 AC1 34 TYR A 155 LYS A 159 PHE A 182 ASN A 184 SITE 7 AC1 34 VAL A 185 ARG A 196 ASN A 197 HOH A 501 SITE 8 AC1 34 HOH A 528 HOH A 547 HOH A 600 HOH A 619 SITE 9 AC1 34 HOH A 624 HOH A 642 SITE 1 AC2 22 ASN A 91 CME A 131 ASN A 184 ASN A 197 SITE 2 AC2 22 VAL A 198 PHE A 202 PRO A 213 ILE A 214 SITE 3 AC2 22 THR A 215 ARG A 222 VAL A 258 ARG A 281 SITE 4 AC2 22 ASP A 284 HOH A 505 HOH A 509 HOH A 569 SITE 5 AC2 22 HOH A 591 HOH A 604 HOH A 608 HOH A 637 SITE 6 AC2 22 HOH A 641 HOH A 660 SITE 1 AC3 6 ASP A 68 GLU A 69 LYS A 72 GLU A 99 SITE 2 AC3 6 LYS A 111 HOH A 516 SITE 1 AC4 3 SER A 25 PRO A 188 HOH A 663 SITE 1 AC5 4 GLU A 144 HIS A 145 HOH A 508 HOH A 578 SITE 1 AC6 6 THR A 254 HIS A 256 SER A 307 PHE A 308 SITE 2 AC6 6 HOH A 502 HOH A 548 CRYST1 89.311 89.311 174.695 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 0.011197 0.006464 0.000000 0.00000 SCALE2 0.000000 0.012929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005724 0.00000