HEADER ISOMERASE 22-SEP-17 5YFW TITLE CRYSTAL STRUCTURE OF RIBOSE-1,5-BISPHOSPHATE ISOMERASE MUTANT D204N TITLE 2 FROM PYROCOCCUS HORIKOSHII OT3 IN COMPLEX WITH RIBOSE-1,5- TITLE 3 BISPHOSPHATE AND AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSE 1,5-BISPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B, C; COMPND 4 EC: 5.3.1.29; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 5 ATCC: ATCC 700860; SOURCE 6 GENE: PH0208; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS ISOMERASE, NMP DEGRADATION PATHWAY, RIBOSE-1, 5-BISPHOSPHATE, KEYWDS 2 ROSSMANN-LIKE FOLD EXPDTA X-RAY DIFFRACTION AUTHOR P.GOGOI,S.P.KANAUJIA REVDAT 3 22-NOV-23 5YFW 1 HETSYN REVDAT 2 29-JUL-20 5YFW 1 REMARK LINK SITE REVDAT 1 14-FEB-18 5YFW 0 JRNL AUTH P.GOGOI,S.P.KANAUJIA JRNL TITL A PRESUMED HOMOLOGUE OF THE REGULATORY SUBUNITS OF EIF2B JRNL TITL 2 FUNCTIONS AS RIBOSE-1,5-BISPHOSPHATE ISOMERASE IN PYROCOCCUS JRNL TITL 3 HORIKOSHII OT3. JRNL REF SCI REP V. 8 1891 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29382938 JRNL DOI 10.1038/S41598-018-20418-W REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56879 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3065 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4157 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 223 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.74000 REMARK 3 B22 (A**2) : 0.74000 REMARK 3 B33 (A**2) : -2.41000 REMARK 3 B12 (A**2) : 0.37000 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): 0.219 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7954 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7815 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10793 ; 1.900 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18048 ; 1.037 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 971 ; 6.399 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 319 ;38.175 ;24.263 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1456 ;16.033 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;18.691 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1227 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8620 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1650 ; 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): 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 5YFW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.28 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60020 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 85.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.1 REMARK 200 STARTING MODEL: 5YFJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.7 M NACL, 3% PEG 6000, 20% MPD, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-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 -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 85.51700 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 171.03400 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 171.03400 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.51700 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 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 63490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 98.70000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 598.61900 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 GLY A 2 REMARK 465 MET B 1 REMARK 465 GLY B 2 REMARK 465 MET C 1 REMARK 465 GLY C 2 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 GLU B 323 O HOH B 501 2.07 REMARK 500 O HOH A 599 O HOH A 605 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 65 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 124 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 190 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 76 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 76 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 MET B 144 CG - SD - CE ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 162 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG C 81 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C 124 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP C 127 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG C 162 NE - CZ - NH1 ANGL. DEV. = 3.3 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 4 66.54 82.51 REMARK 500 ASN A 63 39.09 -84.90 REMARK 500 THR A 64 -72.85 -105.23 REMARK 500 CYS A 135 -151.91 52.09 REMARK 500 THR A 161 76.03 63.35 REMARK 500 PHE A 312 -33.73 -138.75 REMARK 500 PRO A 321 5.43 -68.85 REMARK 500 ASN B 63 36.56 -85.79 REMARK 500 THR B 64 -72.23 -101.88 REMARK 500 CYS B 135 -155.06 55.97 REMARK 500 THR B 161 72.74 61.68 REMARK 500 ILE B 216 121.95 -38.21 REMARK 500 THR C 64 -70.60 -92.40 REMARK 500 LEU C 92 -70.63 -49.37 REMARK 500 CYS C 135 -152.39 49.98 REMARK 500 THR C 161 73.18 61.24 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 ALA A 3 MET A 4 148.14 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 662 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 663 DISTANCE = 6.85 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 K A 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 193 O REMARK 620 2 LYS A 194 O 75.9 REMARK 620 3 THR A 196 O 74.8 106.7 REMARK 620 4 HOH A 602 O 94.3 96.1 151.1 REMARK 620 5 HOH A 620 O 136.9 63.8 101.7 104.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 193 O REMARK 620 2 LYS B 194 O 71.3 REMARK 620 3 THR B 196 O 75.2 107.4 REMARK 620 4 HOH B 632 O 90.2 87.9 153.5 REMARK 620 5 HOH C 600 O 138.8 71.0 100.9 104.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K C 403 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET C 193 O REMARK 620 2 LYS C 194 O 74.6 REMARK 620 3 THR C 196 O 72.1 105.5 REMARK 620 4 HOH C 587 O 126.4 58.3 95.8 REMARK 620 5 HOH C 606 O 92.7 87.4 156.1 108.2 REMARK 620 N 1 2 3 4 DBREF 5YFW A 1 324 UNP O57947 R15PI_PYRHO 1 324 DBREF 5YFW B 1 324 UNP O57947 R15PI_PYRHO 1 324 DBREF 5YFW C 1 324 UNP O57947 R15PI_PYRHO 1 324 SEQADV 5YFW ASN A 204 UNP O57947 ASP 204 ENGINEERED MUTATION SEQADV 5YFW ASN B 204 UNP O57947 ASP 204 ENGINEERED MUTATION SEQADV 5YFW ASN C 204 UNP O57947 ASP 204 ENGINEERED MUTATION SEQRES 1 A 324 MET GLY ALA MET ILE VAL LYS GLU VAL TYR GLU THR ALA SEQRES 2 A 324 GLU LYS ILE LYS SER MET GLU ILE ARG GLY ALA GLY ARG SEQRES 3 A 324 ILE ALA ARG ALA ALA ALA GLN ALA LEU MET ILE GLN ALA SEQRES 4 A 324 GLU LYS SER LYS ALA LYS GLU PRO GLU GLU LEU TRP ASN SEQRES 5 A 324 GLU LEU LYS VAL ALA SER LYS ILE LEU TYR ASN THR ARG SEQRES 6 A 324 PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR VAL SEQRES 7 A 324 MET HIS ARG VAL LYS ALA ALA TYR LEU GLY GLY ALA ASP SEQRES 8 A 324 LEU GLU THR LEU ARG PHE THR ALA ILE ASN SER ALA LYS SEQRES 9 A 324 GLU PHE ILE TYR ASN SER GLU LYS ALA ILE GLU ARG ILE SEQRES 10 A 324 GLY GLU ILE GLY ALA LYS ARG ILE GLU ASP GLY ASP ILE SEQRES 11 A 324 ILE MET THR HIS CYS HIS SER LYS ALA ALA ILE SER VAL SEQRES 12 A 324 MET LYS LYS ALA PHE GLU GLN GLY LYS ASN ILE LYS VAL SEQRES 13 A 324 ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS ILE SEQRES 14 A 324 THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL ILE SEQRES 15 A 324 TYR ILE VAL ASP SER ALA ALA ARG HIS TYR MET LYS MET SEQRES 16 A 324 THR ASP LYS VAL VAL MET GLY ALA ASN SER ILE THR ALA SEQRES 17 A 324 ASN GLY ALA VAL ILE ASN LYS ILE GLY THR SER LEU ILE SEQRES 18 A 324 ALA LEU THR ALA LYS GLU HIS ARG VAL TRP VAL MET ILE SEQRES 19 A 324 ALA ALA GLU THR TYR LYS PHE HIS PRO ALA THR MET LEU SEQRES 20 A 324 GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR GLU SEQRES 21 A 324 VAL ILE PRO GLU GLU GLU LEU ARG THR TRP PRO LYS ASN SEQRES 22 A 324 ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO PRO SEQRES 23 A 324 GLU TYR ILE ASP VAL ILE ILE THR GLU ARG GLY ILE ILE SEQRES 24 A 324 PRO PRO TYR ALA ALA ILE ASP ILE LEU LYS GLU GLU PHE SEQRES 25 A 324 GLY TRP ALA LEU LYS TYR LYS GLU PRO TRP GLU ASP SEQRES 1 B 324 MET GLY ALA MET ILE VAL LYS GLU VAL TYR GLU THR ALA SEQRES 2 B 324 GLU LYS ILE LYS SER MET GLU ILE ARG GLY ALA GLY ARG SEQRES 3 B 324 ILE ALA ARG ALA ALA ALA GLN ALA LEU MET ILE GLN ALA SEQRES 4 B 324 GLU LYS SER LYS ALA LYS GLU PRO GLU GLU LEU TRP ASN SEQRES 5 B 324 GLU LEU LYS VAL ALA SER LYS ILE LEU TYR ASN THR ARG SEQRES 6 B 324 PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR VAL SEQRES 7 B 324 MET HIS ARG VAL LYS ALA ALA TYR LEU GLY GLY ALA ASP SEQRES 8 B 324 LEU GLU THR LEU ARG PHE THR ALA ILE ASN SER ALA LYS SEQRES 9 B 324 GLU PHE ILE TYR ASN SER GLU LYS ALA ILE GLU ARG ILE SEQRES 10 B 324 GLY GLU ILE GLY ALA LYS ARG ILE GLU ASP GLY ASP ILE SEQRES 11 B 324 ILE MET THR HIS CYS HIS SER LYS ALA ALA ILE SER VAL SEQRES 12 B 324 MET LYS LYS ALA PHE GLU GLN GLY LYS ASN ILE LYS VAL SEQRES 13 B 324 ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS ILE SEQRES 14 B 324 THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL ILE SEQRES 15 B 324 TYR ILE VAL ASP SER ALA ALA ARG HIS TYR MET LYS MET SEQRES 16 B 324 THR ASP LYS VAL VAL MET GLY ALA ASN SER ILE THR ALA SEQRES 17 B 324 ASN GLY ALA VAL ILE ASN LYS ILE GLY THR SER LEU ILE SEQRES 18 B 324 ALA LEU THR ALA LYS GLU HIS ARG VAL TRP VAL MET ILE SEQRES 19 B 324 ALA ALA GLU THR TYR LYS PHE HIS PRO ALA THR MET LEU SEQRES 20 B 324 GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR GLU SEQRES 21 B 324 VAL ILE PRO GLU GLU GLU LEU ARG THR TRP PRO LYS ASN SEQRES 22 B 324 ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO PRO SEQRES 23 B 324 GLU TYR ILE ASP VAL ILE ILE THR GLU ARG GLY ILE ILE SEQRES 24 B 324 PRO PRO TYR ALA ALA ILE ASP ILE LEU LYS GLU GLU PHE SEQRES 25 B 324 GLY TRP ALA LEU LYS TYR LYS GLU PRO TRP GLU ASP SEQRES 1 C 324 MET GLY ALA MET ILE VAL LYS GLU VAL TYR GLU THR ALA SEQRES 2 C 324 GLU LYS ILE LYS SER MET GLU ILE ARG GLY ALA GLY ARG SEQRES 3 C 324 ILE ALA ARG ALA ALA ALA GLN ALA LEU MET ILE GLN ALA SEQRES 4 C 324 GLU LYS SER LYS ALA LYS GLU PRO GLU GLU LEU TRP ASN SEQRES 5 C 324 GLU LEU LYS VAL ALA SER LYS ILE LEU TYR ASN THR ARG SEQRES 6 C 324 PRO THR ALA VAL SER LEU PRO ASN ALA LEU ARG TYR VAL SEQRES 7 C 324 MET HIS ARG VAL LYS ALA ALA TYR LEU GLY GLY ALA ASP SEQRES 8 C 324 LEU GLU THR LEU ARG PHE THR ALA ILE ASN SER ALA LYS SEQRES 9 C 324 GLU PHE ILE TYR ASN SER GLU LYS ALA ILE GLU ARG ILE SEQRES 10 C 324 GLY GLU ILE GLY ALA LYS ARG ILE GLU ASP GLY ASP ILE SEQRES 11 C 324 ILE MET THR HIS CYS HIS SER LYS ALA ALA ILE SER VAL SEQRES 12 C 324 MET LYS LYS ALA PHE GLU GLN GLY LYS ASN ILE LYS VAL SEQRES 13 C 324 ILE VAL THR GLU THR ARG PRO LYS TRP GLN GLY LYS ILE SEQRES 14 C 324 THR ALA LYS GLU LEU ALA SER TYR GLY ILE PRO VAL ILE SEQRES 15 C 324 TYR ILE VAL ASP SER ALA ALA ARG HIS TYR MET LYS MET SEQRES 16 C 324 THR ASP LYS VAL VAL MET GLY ALA ASN SER ILE THR ALA SEQRES 17 C 324 ASN GLY ALA VAL ILE ASN LYS ILE GLY THR SER LEU ILE SEQRES 18 C 324 ALA LEU THR ALA LYS GLU HIS ARG VAL TRP VAL MET ILE SEQRES 19 C 324 ALA ALA GLU THR TYR LYS PHE HIS PRO ALA THR MET LEU SEQRES 20 C 324 GLY GLN LEU VAL GLU ILE GLU MET ARG ASP PRO THR GLU SEQRES 21 C 324 VAL ILE PRO GLU GLU GLU LEU ARG THR TRP PRO LYS ASN SEQRES 22 C 324 ILE GLU VAL TRP ASN PRO ALA PHE ASP VAL THR PRO PRO SEQRES 23 C 324 GLU TYR ILE ASP VAL ILE ILE THR GLU ARG GLY ILE ILE SEQRES 24 C 324 PRO PRO TYR ALA ALA ILE ASP ILE LEU LYS GLU GLU PHE SEQRES 25 C 324 GLY TRP ALA LEU LYS TYR LYS GLU PRO TRP GLU ASP HET RI2 A 401 18 HET AMP A 402 23 HET K A 403 1 HET RI2 B 401 18 HET AMP B 402 23 HET K B 403 1 HET MRD B 404 8 HET RI2 C 401 18 HET AMP C 402 23 HET K C 403 1 HETNAM RI2 1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOFURANOSE HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM K POTASSIUM ION HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL HETSYN RI2 1,5-DI-O-PHOSPHONO-ALPHA-D-RIBOSE; 1,5-DI-O-PHOSPHONO- HETSYN 2 RI2 D-RIBOSE; 1,5-DI-O-PHOSPHONO-RIBOSE FORMUL 4 RI2 3(C5 H12 O11 P2) FORMUL 5 AMP 3(C10 H14 N5 O7 P) FORMUL 6 K 3(K 1+) FORMUL 10 MRD C6 H14 O2 FORMUL 14 HOH *464(H2 O) HELIX 1 AA1 VAL A 6 SER A 18 1 13 HELIX 2 AA2 GLY A 23 SER A 42 1 20 HELIX 3 AA3 GLU A 46 ASN A 63 1 18 HELIX 4 AA4 VAL A 69 GLY A 88 1 20 HELIX 5 AA5 ASP A 91 ALA A 122 1 32 HELIX 6 AA6 LYS A 123 ILE A 125 5 3 HELIX 7 AA7 SER A 137 GLN A 150 1 14 HELIX 8 AA8 TRP A 165 TYR A 177 1 13 HELIX 9 AA9 VAL A 185 ALA A 189 5 5 HELIX 10 AB1 TYR A 192 THR A 196 5 5 HELIX 11 AB2 GLY A 217 HIS A 228 1 12 HELIX 12 AB3 GLU A 237 PHE A 241 5 5 HELIX 13 AB4 HIS A 242 GLY A 248 5 7 HELIX 14 AB5 ASP A 257 VAL A 261 5 5 HELIX 15 AB6 PRO A 263 ARG A 268 1 6 HELIX 16 AB7 PRO A 285 ILE A 289 5 5 HELIX 17 AB8 PRO A 300 TYR A 302 5 3 HELIX 18 AB9 ALA A 303 PHE A 312 1 10 HELIX 19 AC1 GLY A 313 TYR A 318 5 6 HELIX 20 AC2 VAL B 6 SER B 18 1 13 HELIX 21 AC3 GLY B 23 SER B 42 1 20 HELIX 22 AC4 GLU B 46 ASN B 63 1 18 HELIX 23 AC5 VAL B 69 GLY B 88 1 20 HELIX 24 AC6 ASP B 91 LYS B 123 1 33 HELIX 25 AC7 SER B 137 GLN B 150 1 14 HELIX 26 AC8 TRP B 165 TYR B 177 1 13 HELIX 27 AC9 VAL B 185 ALA B 189 5 5 HELIX 28 AD1 TYR B 192 THR B 196 5 5 HELIX 29 AD2 GLY B 217 HIS B 228 1 12 HELIX 30 AD3 GLU B 237 PHE B 241 5 5 HELIX 31 AD4 HIS B 242 GLY B 248 5 7 HELIX 32 AD5 ASP B 257 VAL B 261 5 5 HELIX 33 AD6 PRO B 263 THR B 269 1 7 HELIX 34 AD7 PRO B 285 ILE B 289 5 5 HELIX 35 AD8 PRO B 300 TYR B 302 5 3 HELIX 36 AD9 ALA B 303 PHE B 312 1 10 HELIX 37 AE1 GLY B 313 TYR B 318 5 6 HELIX 38 AE2 VAL C 6 SER C 18 1 13 HELIX 39 AE3 GLY C 23 SER C 42 1 20 HELIX 40 AE4 GLU C 46 ASN C 63 1 18 HELIX 41 AE5 VAL C 69 GLY C 88 1 20 HELIX 42 AE6 ASP C 91 LYS C 123 1 33 HELIX 43 AE7 SER C 137 GLN C 150 1 14 HELIX 44 AE8 TRP C 165 TYR C 177 1 13 HELIX 45 AE9 VAL C 185 ALA C 189 5 5 HELIX 46 AF1 TYR C 192 THR C 196 5 5 HELIX 47 AF2 GLY C 217 HIS C 228 1 12 HELIX 48 AF3 GLU C 237 PHE C 241 5 5 HELIX 49 AF4 HIS C 242 GLY C 248 5 7 HELIX 50 AF5 ASP C 257 VAL C 261 5 5 HELIX 51 AF6 PRO C 263 ARG C 268 1 6 HELIX 52 AF7 PRO C 285 ILE C 289 5 5 HELIX 53 AF8 PRO C 300 TYR C 302 5 3 HELIX 54 AF9 ALA C 303 PHE C 312 1 10 HELIX 55 AG1 GLY C 313 TYR C 318 5 6 SHEET 1 AA1 7 VAL A 181 ILE A 184 0 SHEET 2 AA1 7 LYS A 155 THR A 159 1 N VAL A 156 O ILE A 182 SHEET 3 AA1 7 ILE A 130 THR A 133 1 N ILE A 131 O ILE A 157 SHEET 4 AA1 7 LYS A 198 MET A 201 1 O LYS A 198 N MET A 132 SHEET 5 AA1 7 TRP A 231 ALA A 235 1 O MET A 233 N VAL A 199 SHEET 6 AA1 7 VAL A 291 THR A 294 1 O VAL A 291 N ILE A 234 SHEET 7 AA1 7 GLY A 297 ILE A 299 -1 O ILE A 299 N ILE A 292 SHEET 1 AA2 3 SER A 205 ILE A 206 0 SHEET 2 AA2 3 VAL A 212 LYS A 215 -1 O ILE A 213 N SER A 205 SHEET 3 AA2 3 PHE A 281 THR A 284 -1 O THR A 284 N VAL A 212 SHEET 1 AA3 7 VAL B 181 ILE B 184 0 SHEET 2 AA3 7 LYS B 155 THR B 159 1 N VAL B 158 O ILE B 182 SHEET 3 AA3 7 ILE B 130 THR B 133 1 N ILE B 131 O LYS B 155 SHEET 4 AA3 7 LYS B 198 MET B 201 1 O LYS B 198 N MET B 132 SHEET 5 AA3 7 TRP B 231 ALA B 235 1 O TRP B 231 N VAL B 199 SHEET 6 AA3 7 VAL B 291 THR B 294 1 O ILE B 293 N ILE B 234 SHEET 7 AA3 7 GLY B 297 ILE B 299 -1 O ILE B 299 N ILE B 292 SHEET 1 AA4 3 SER B 205 ILE B 206 0 SHEET 2 AA4 3 VAL B 212 LYS B 215 -1 O ILE B 213 N SER B 205 SHEET 3 AA4 3 PHE B 281 THR B 284 -1 O THR B 284 N VAL B 212 SHEET 1 AA5 7 VAL C 181 ILE C 184 0 SHEET 2 AA5 7 LYS C 155 THR C 159 1 N VAL C 156 O ILE C 182 SHEET 3 AA5 7 ILE C 130 THR C 133 1 N ILE C 131 O ILE C 157 SHEET 4 AA5 7 LYS C 198 MET C 201 1 O VAL C 200 N MET C 132 SHEET 5 AA5 7 TRP C 231 ALA C 235 1 O TRP C 231 N VAL C 199 SHEET 6 AA5 7 VAL C 291 THR C 294 1 O ILE C 293 N ILE C 234 SHEET 7 AA5 7 GLY C 297 ILE C 299 -1 O ILE C 299 N ILE C 292 SHEET 1 AA6 3 SER C 205 ILE C 206 0 SHEET 2 AA6 3 VAL C 212 LYS C 215 -1 O ILE C 213 N SER C 205 SHEET 3 AA6 3 PHE C 281 THR C 284 -1 O THR C 284 N VAL C 212 LINK O MET A 193 K K A 403 1555 1555 3.09 LINK O LYS A 194 K K A 403 1555 1555 2.98 LINK O THR A 196 K K A 403 1555 1555 2.73 LINK K K A 403 O HOH A 602 1555 1555 2.78 LINK K K A 403 O HOH A 620 1555 1555 2.88 LINK O MET B 193 K K B 403 1555 1555 3.19 LINK O LYS B 194 K K B 403 1555 1555 3.00 LINK O THR B 196 K K B 403 1555 1555 2.78 LINK K K B 403 O HOH B 632 1555 1555 2.63 LINK K K B 403 O HOH C 600 1555 5657 2.93 LINK O MET C 193 K K C 403 1555 1555 3.09 LINK O LYS C 194 K K C 403 1555 1555 3.03 LINK O THR C 196 K K C 403 1555 1555 2.61 LINK K K C 403 O HOH C 587 1555 1555 3.09 LINK K K C 403 O HOH C 606 1555 1555 2.70 CISPEP 1 ARG A 162 PRO A 163 0 -0.01 CISPEP 2 ARG B 162 PRO B 163 0 0.66 CISPEP 3 ARG C 162 PRO C 163 0 -4.13 CRYST1 98.700 98.700 256.551 90.00 90.00 120.00 P 31 1 2 18 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 0.010132 0.005850 0.000000 0.00000 SCALE2 0.000000 0.011699 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003898 0.00000