HEADER ISOMERASE 05-DEC-07 2ZE3 TITLE CRYSTAL STRUCTURE OF DFA0005 COMPLEXED WITH ALPHA-KETOGLUTARATE: A TITLE 2 NOVEL MEMBER OF THE ICL/PEPM SUPERFAMILY FROM ALKALI-TOLERANT TITLE 3 DEINOCOCCUS FICUS CAVEAT 2ZE3 CHIRALITY ERRORS AT CA CENTER OF MET 1, ARG 275 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DFA0005; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINOCOCCUS FICUS; SOURCE 3 ORGANISM_TAXID: 317577; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEINOCOCCUS FICUS, ORGANIC WASTE LEFT-OVER DECOMPOSITION, KEYWDS 2 ALKALIPHILIC, ICL/PEPM SUPERFAMILY, ALPHA-KETOGLUTARATE LIGAND, KEYWDS 3 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.J.LIAO,K.H.CHIN,S.H.CHOU REVDAT 5 13-MAR-24 2ZE3 1 REMARK REVDAT 4 13-JUL-11 2ZE3 1 VERSN REVDAT 3 24-FEB-09 2ZE3 1 VERSN REVDAT 2 04-NOV-08 2ZE3 1 JRNL REVDAT 1 12-AUG-08 2ZE3 0 JRNL AUTH C.J.LIAO,K.H.CHIN,C.H.LIN,P.S.TSAI,P.C.LYU,C.C.YOUNG, JRNL AUTH 2 A.H.WANG,S.H.CHOU JRNL TITL CRYSTAL STRUCTURE OF DFA0005 COMPLEXED WITH JRNL TITL 2 ALPHA-KETOGLUTARATE: A NOVEL MEMBER OF THE ICL/PEPM JRNL TITL 3 SUPERFAMILY FROM ALKALI-TOLERANT DEINOCOCCUS FICUS JRNL REF PROTEINS V. 73 362 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18433062 JRNL DOI 10.1002/PROT.22071 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 223849.250 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 90686 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 SET) : 0.223 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 8686 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13545 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 1509 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.008 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2061 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 253 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.10000 REMARK 3 B22 (A**2) : -2.10000 REMARK 3 B33 (A**2) : 4.21000 REMARK 3 B12 (A**2) : 0.19000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.20 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 BOND ANGLES (DEGREES) : 2.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 5.730 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.940 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.440 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.870 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 43.58 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000027855. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 189632 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 57.05900 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 57.05900 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 57.05900 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 57.05900 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 57.05900 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 57.05900 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: 6250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 57.05900 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 366 LIES ON A SPECIAL POSITION. 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 OG SER A 261 O HOH A 526 1.99 REMARK 500 O HOH A 431 O HOH A 494 2.06 REMARK 500 O HOH A 445 O HOH A 517 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 482 O HOH A 482 12555 1.12 REMARK 500 O HOH A 372 O HOH A 372 2655 1.16 REMARK 500 O HOH A 481 O HOH A 481 2655 1.37 REMARK 500 O HOH A 354 O HOH A 354 12555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 1 CA MET A 1 C -0.224 REMARK 500 THR A 2 N THR A 2 CA -0.223 REMARK 500 THR A 2 CA THR A 2 CB 0.208 REMARK 500 ARG A 30 CD ARG A 30 NE -0.154 REMARK 500 GLY A 52 N GLY A 52 CA -0.207 REMARK 500 ARG A 53 N ARG A 53 CA 0.233 REMARK 500 ARG A 53 CB ARG A 53 CG -0.351 REMARK 500 ARG A 53 CG ARG A 53 CD -0.225 REMARK 500 ARG A 53 CD ARG A 53 NE -0.332 REMARK 500 GLU A 69 CB GLU A 69 CG 0.191 REMARK 500 LEU A 125 CB LEU A 125 CG 0.203 REMARK 500 GLY A 158 CA GLY A 158 C -0.108 REMARK 500 GLY A 158 C HIS A 159 N 0.209 REMARK 500 HIS A 159 N HIS A 159 CA 0.183 REMARK 500 GLY A 160 CA GLY A 160 C -0.102 REMARK 500 GLY A 160 C ALA A 161 N 0.142 REMARK 500 ALA A 161 N ALA A 161 CA 0.212 REMARK 500 ARG A 219 CD ARG A 219 NE -0.331 REMARK 500 GLY A 267 N GLY A 267 CA -0.139 REMARK 500 GLY A 267 CA GLY A 267 C -0.212 REMARK 500 HIS A 274 C ARG A 275 N 0.262 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 MET A 1 CB - CA - C ANGL. DEV. = 20.9 DEGREES REMARK 500 MET A 1 CA - C - N ANGL. DEV. = -14.7 DEGREES REMARK 500 THR A 43 CA - CB - CG2 ANGL. DEV. = 9.9 DEGREES REMARK 500 GLY A 52 CA - C - O ANGL. DEV. = 19.6 DEGREES REMARK 500 GLY A 52 CA - C - N ANGL. DEV. = -23.0 DEGREES REMARK 500 ARG A 53 C - N - CA ANGL. DEV. = -17.8 DEGREES REMARK 500 ARG A 53 CB - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 53 N - CA - CB ANGL. DEV. = 31.3 DEGREES REMARK 500 ARG A 53 CA - CB - CG ANGL. DEV. = 34.5 DEGREES REMARK 500 ARG A 53 CB - CG - CD ANGL. DEV. = 40.1 DEGREES REMARK 500 ARG A 53 CG - CD - NE ANGL. DEV. = 19.1 DEGREES REMARK 500 ARG A 53 CD - NE - CZ ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG A 53 N - CA - C ANGL. DEV. = -22.0 DEGREES REMARK 500 GLU A 69 CB - CG - CD ANGL. DEV. = 25.8 DEGREES REMARK 500 LEU A 125 CB - CG - CD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 GLY A 158 N - CA - C ANGL. DEV. = 36.7 DEGREES REMARK 500 GLY A 158 CA - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 HIS A 159 N - CA - CB ANGL. DEV. = -17.2 DEGREES REMARK 500 HIS A 159 N - CA - C ANGL. DEV. = 18.9 DEGREES REMARK 500 ARG A 219 CG - CD - NE ANGL. DEV. = 22.6 DEGREES REMARK 500 ARG A 219 CD - NE - CZ ANGL. DEV. = 13.0 DEGREES REMARK 500 MET A 236 CG - SD - CE ANGL. DEV. = -15.5 DEGREES REMARK 500 GLU A 268 N - CA - CB ANGL. DEV. = 12.6 DEGREES REMARK 500 HIS A 274 CA - C - O ANGL. DEV. = 16.8 DEGREES REMARK 500 ARG A 275 N - CA - CB ANGL. DEV. = 18.2 DEGREES REMARK 500 ARG A 275 CA - C - O ANGL. DEV. = -27.5 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 ARG A 53 -2.32 174.49 REMARK 500 ASP A 55 79.48 -15.26 REMARK 500 THR A 58 -151.88 64.63 REMARK 500 GLU A 84 -128.45 48.76 REMARK 500 ALA A 161 -67.91 81.35 REMARK 500 LEU A 189 11.30 82.35 REMARK 500 GLU A 268 -69.27 -21.46 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 GLY A 267 GLU A 268 141.92 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 A 53 0.08 SIDE CHAIN 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 AKG A 276 DBREF 2ZE3 A 1 275 PDB 2ZE3 2ZE3 1 275 SEQRES 1 A 275 MET THR HIS ALA ASP HIS ALA ARG SER PHE HIS ALA LEU SEQRES 2 A 275 HIS GLN THR GLY PHE LEU LEU PRO ASN ALA TRP ASP VAL SEQRES 3 A 275 ALA SER ALA ARG LEU LEU GLU ALA ALA GLY PHE THR ALA SEQRES 4 A 275 ILE GLY THR THR SER ALA GLY ILE ALA HIS ALA ARG GLY SEQRES 5 A 275 ARG THR ASP GLY GLN THR LEU THR ARG ASP GLU MET GLY SEQRES 6 A 275 ARG GLU VAL GLU ALA ILE VAL ARG ALA VAL ALA ILE PRO SEQRES 7 A 275 VAL ASN ALA ASP ILE GLU ALA GLY TYR GLY HIS ALA PRO SEQRES 8 A 275 GLU ASP VAL ARG ARG THR VAL GLU HIS PHE ALA ALA LEU SEQRES 9 A 275 GLY VAL ALA GLY VAL ASN LEU GLU ASP ALA THR GLY LEU SEQRES 10 A 275 THR PRO THR GLU LEU TYR ASP LEU ASP SER GLN LEU ARG SEQRES 11 A 275 ARG ILE GLU ALA ALA ARG ALA ALA ILE ASP ALA SER GLY SEQRES 12 A 275 VAL PRO VAL PHE LEU ASN ALA ARG THR ASP THR PHE LEU SEQRES 13 A 275 LYS GLY HIS GLY ALA THR ASP GLU GLU ARG LEU ALA GLU SEQRES 14 A 275 THR VAL ARG ARG GLY GLN ALA TYR ALA ASP ALA GLY ALA SEQRES 15 A 275 ASP GLY ILE PHE VAL PRO LEU ALA LEU GLN SER GLN ASP SEQRES 16 A 275 ILE ARG ALA LEU ALA ASP ALA LEU ARG VAL PRO LEU ASN SEQRES 17 A 275 VAL MET ALA PHE PRO GLY SER PRO VAL PRO ARG ALA LEU SEQRES 18 A 275 LEU ASP ALA GLY ALA ALA ARG VAL SER PHE GLY GLN SER SEQRES 19 A 275 LEU MET LEU ALA THR LEU GLY LEU VAL GLN ARG MET ALA SEQRES 20 A 275 ALA GLU LEU HIS ALA ALA GLU GLN SER PRO LEU MET ASP SEQRES 21 A 275 SER TYR PHE LEU GLY PHE GLY GLU GLY HIS ASP LEU PHE SEQRES 22 A 275 HIS ARG HET AKG A 276 10 HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 AKG C5 H6 O5 FORMUL 3 HOH *253(H2 O) HELIX 1 1 MET A 1 GLY A 17 1 17 HELIX 2 2 ASP A 25 GLY A 36 1 12 HELIX 3 3 THR A 43 ARG A 51 1 9 HELIX 4 4 THR A 60 VAL A 75 1 16 HELIX 5 5 ALA A 90 LEU A 104 1 15 HELIX 6 6 ASP A 124 GLY A 143 1 20 HELIX 7 7 THR A 162 ALA A 180 1 19 HELIX 8 8 GLN A 192 LEU A 203 1 12 HELIX 9 9 VAL A 217 ALA A 224 1 8 HELIX 10 10 GLN A 233 GLU A 254 1 22 HELIX 11 11 SER A 256 PHE A 266 1 11 HELIX 12 12 PHE A 266 ARG A 275 1 10 SHEET 1 A 9 PHE A 18 LEU A 20 0 SHEET 2 A 9 ARG A 228 SER A 230 1 O VAL A 229 N LEU A 20 SHEET 3 A 9 LEU A 207 MET A 210 1 N VAL A 209 O ARG A 228 SHEET 4 A 9 GLY A 184 PHE A 186 1 N ILE A 185 O ASN A 208 SHEET 5 A 9 PHE A 147 ARG A 151 1 N ALA A 150 O GLY A 184 SHEET 6 A 9 GLY A 108 GLU A 112 1 N VAL A 109 O PHE A 147 SHEET 7 A 9 VAL A 79 ASP A 82 1 N ALA A 81 O GLY A 108 SHEET 8 A 9 ILE A 40 THR A 42 1 N ILE A 40 O ASN A 80 SHEET 9 A 9 ASN A 22 ALA A 23 1 N ALA A 23 O GLY A 41 SITE 1 AC1 12 ASN A 22 THR A 43 SER A 44 ALA A 45 SITE 2 AC1 12 ASP A 82 ASN A 110 ARG A 151 SER A 230 SITE 3 AC1 12 GLY A 232 HOH A 302 HOH A 460 HOH A 462 CRYST1 108.840 108.840 114.118 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 0.009188 0.005305 0.000000 0.00000 SCALE2 0.000000 0.010609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008763 0.00000