HEADER OXIDOREDUCTASE 28-JAN-19 6QK0 TITLE R2-LIKE LIGAND-BINDING OXIDASE E69D MUTANT WITH ANAEROBICALLY TITLE 2 RECONSTITUTED MN/FE COFACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.17.4.1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS KAUSTOPHILUS (STRAIN HTA426); SOURCE 3 ORGANISM_TAXID: 235909; SOURCE 4 STRAIN: HTA426; SOURCE 5 GENE: GK2771; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-46 EK/LIC KEYWDS R2-LIKE LIGAND-BINDING OXIDASE, MN/FE COFACTOR, RIBONUCLEOTIDE KEYWDS 2 REDUCTASE R2 SUBUNIT FOLD, METALLOPROTEIN OXIDOREDUCTASE, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.GRIESE,M.HOGBOM REVDAT 3 24-JAN-24 6QK0 1 REMARK REVDAT 2 26-AUG-20 6QK0 1 JRNL LINK REVDAT 1 19-FEB-20 6QK0 0 JRNL AUTH E.C.KISGEROPOULOS,J.J.GRIESE,Z.R.SMITH,R.M.M.BRANCA, JRNL AUTH 2 C.R.SCHNEIDER,M.HOGBOM,H.S.SHAFAAT JRNL TITL KEY STRUCTURAL MOTIFS BALANCE METAL BINDING AND OXIDATIVE JRNL TITL 2 REACTIVITY IN A HETEROBIMETALLIC MN/FE PROTEIN. JRNL REF J.AM.CHEM.SOC. V. 142 5338 2020 JRNL REFN ESSN 1520-5126 JRNL PMID 32062969 JRNL DOI 10.1021/JACS.0C00333 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 40492 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.6145 - 5.0376 0.96 2841 150 0.1764 0.2172 REMARK 3 2 5.0376 - 3.9991 0.97 2777 146 0.1542 0.2088 REMARK 3 3 3.9991 - 3.4937 0.97 2759 145 0.1848 0.2365 REMARK 3 4 3.4937 - 3.1743 0.98 2801 147 0.2020 0.2298 REMARK 3 5 3.1743 - 2.9469 0.99 2798 147 0.2277 0.3231 REMARK 3 6 2.9469 - 2.7731 0.99 2819 149 0.2269 0.2947 REMARK 3 7 2.7731 - 2.6343 0.98 2775 146 0.2434 0.2724 REMARK 3 8 2.6343 - 2.5196 0.99 2770 146 0.2291 0.3028 REMARK 3 9 2.5196 - 2.4226 0.99 2795 147 0.2411 0.3078 REMARK 3 10 2.4226 - 2.3390 0.99 2792 147 0.2551 0.3304 REMARK 3 11 2.3390 - 2.2659 0.97 2771 146 0.2920 0.3619 REMARK 3 12 2.2659 - 2.2011 0.93 2630 139 0.4300 0.5229 REMARK 3 13 2.2011 - 2.1432 0.97 2726 144 0.3208 0.3293 REMARK 3 14 2.1432 - 2.0909 0.85 2412 127 0.3759 0.4021 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.021 4695 REMARK 3 ANGLE : 1.262 6301 REMARK 3 CHIRALITY : 0.065 659 REMARK 3 PLANARITY : 0.009 808 REMARK 3 DIHEDRAL : 13.073 2778 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40539 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.79900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.650 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: 4HR4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (W/V) PEG 1500, 0.1 M HEPES-NA PH REMARK 280 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 80.40400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.98150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 80.40400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.98150 REMARK 290 SMTRY3 4 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: 6820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.0 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 MET A -13 REMARK 465 ALA A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 VAL A -5 REMARK 465 ASP A -4 REMARK 465 ASP A -3 REMARK 465 ASP A -2 REMARK 465 ASP A -1 REMARK 465 LYS A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 ASP A 5 REMARK 465 GLY A 6 REMARK 465 PHE A 7 REMARK 465 ARG A 288 REMARK 465 VAL A 289 REMARK 465 ASP A 290 REMARK 465 VAL A 291 REMARK 465 VAL A 292 REMARK 465 GLU A 293 REMARK 465 GLY A 294 REMARK 465 LEU A 295 REMARK 465 GLU A 296 REMARK 465 LYS A 297 REMARK 465 THR A 298 REMARK 465 ALA A 299 REMARK 465 ALA A 300 REMARK 465 GLU A 301 REMARK 465 SER A 302 REMARK 465 MET B -13 REMARK 465 ALA B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 VAL B -5 REMARK 465 ASP B -4 REMARK 465 ASP B -3 REMARK 465 ASP B -2 REMARK 465 ASP B -1 REMARK 465 LYS B 0 REMARK 465 MET B 1 REMARK 465 VAL B 2 REMARK 465 HIS B 3 REMARK 465 GLY B 68 REMARK 465 ASP B 69 REMARK 465 GLU B 70 REMARK 465 ALA B 71 REMARK 465 VAL B 72 REMARK 465 GLN B 252 REMARK 465 GLN B 253 REMARK 465 GLN B 254 REMARK 465 LEU B 255 REMARK 465 ALA B 256 REMARK 465 ARG B 257 REMARK 465 THR B 258 REMARK 465 TYR B 259 REMARK 465 ALA B 260 REMARK 465 LEU B 261 REMARK 465 GLU B 262 REMARK 465 LYS B 287 REMARK 465 ARG B 288 REMARK 465 VAL B 289 REMARK 465 ASP B 290 REMARK 465 VAL B 291 REMARK 465 VAL B 292 REMARK 465 GLU B 293 REMARK 465 GLY B 294 REMARK 465 LEU B 295 REMARK 465 GLU B 296 REMARK 465 LYS B 297 REMARK 465 THR B 298 REMARK 465 ALA B 299 REMARK 465 ALA B 300 REMARK 465 GLU B 301 REMARK 465 SER B 302 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 OE2 GLU A 225 HH12 ARG A 285 1.41 REMARK 500 HE21 GLN B 120 O HOH B 501 1.49 REMARK 500 OE2 GLU A 221 HH21 ARG A 285 1.51 REMARK 500 OD1 ASP B 232 HZ1 LYS B 280 1.59 REMARK 500 OD1 ASP A 69 O2 PLM A 403 2.02 REMARK 500 NH1 ARG B 179 OD1 ASP B 196 2.03 REMARK 500 OE2 GLU A 225 NH1 ARG A 285 2.05 REMARK 500 NH2 ARG B 179 OD1 ASN B 199 2.09 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 OE1 GLU A 54 NZ LYS A 274 4746 2.19 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 GLU A 262 CB GLU A 262 CG 0.132 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 88 NE - CZ - NH2 ANGL. DEV. = -3.4 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 LYS A 55 5.46 -65.80 REMARK 500 GLU A 137 -72.35 -121.90 REMARK 500 ALA B 12 -144.07 -151.26 REMARK 500 SER B 66 1.86 -58.12 REMARK 500 GLU B 137 -71.47 -119.70 REMARK 500 THR B 169 -60.48 -121.81 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 69 OD1 REMARK 620 2 GLU A 102 OE1 98.9 REMARK 620 3 HIS A 105 ND1 104.1 88.6 REMARK 620 4 GLU A 202 OE2 152.0 106.0 89.4 REMARK 620 5 PLM A 403 O2 57.5 93.1 161.6 107.6 REMARK 620 6 HOH A 503 O 73.5 169.1 100.7 80.0 76.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 102 OE2 REMARK 620 2 GLU A 167 OE2 91.8 REMARK 620 3 GLU A 202 OE1 166.8 99.9 REMARK 620 4 GLU A 202 OE2 109.2 155.1 58.0 REMARK 620 5 HIS A 205 ND1 78.4 90.7 107.3 106.1 REMARK 620 6 PLM A 403 O1 81.6 87.7 92.8 82.6 159.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 102 OE1 REMARK 620 2 GLU B 102 OE2 56.8 REMARK 620 3 HIS B 105 ND1 84.6 94.3 REMARK 620 4 GLU B 202 OE2 154.7 99.1 106.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 102 OE2 REMARK 620 2 GLU B 167 OE2 113.0 REMARK 620 3 GLU B 202 OE1 94.3 138.3 REMARK 620 4 GLU B 202 OE2 92.9 146.3 54.3 REMARK 620 5 HIS B 205 ND1 84.4 83.7 67.6 121.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 B 404 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 130 NE2 REMARK 620 2 HOH B 532 O 76.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLM A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLM B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 B 404 DBREF 6QK0 A 1 302 UNP Q5KW80 Q5KW80_GEOKA 1 302 DBREF 6QK0 B 1 302 UNP Q5KW80 Q5KW80_GEOKA 1 302 SEQADV 6QK0 MET A -13 UNP Q5KW80 INITIATING METHIONINE SEQADV 6QK0 ALA A -12 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -11 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -10 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -9 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -8 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -7 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS A -6 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 VAL A -5 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP A -4 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP A -3 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP A -2 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP A -1 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 LYS A 0 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP A 69 UNP Q5KW80 GLU 69 ENGINEERED MUTATION SEQADV 6QK0 MET B -13 UNP Q5KW80 INITIATING METHIONINE SEQADV 6QK0 ALA B -12 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -11 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -10 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -9 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -8 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -7 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 HIS B -6 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 VAL B -5 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP B -4 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP B -3 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP B -2 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP B -1 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 LYS B 0 UNP Q5KW80 EXPRESSION TAG SEQADV 6QK0 ASP B 69 UNP Q5KW80 GLU 69 ENGINEERED MUTATION SEQRES 1 A 316 MET ALA HIS HIS HIS HIS HIS HIS VAL ASP ASP ASP ASP SEQRES 2 A 316 LYS MET VAL HIS HIS ASP GLY PHE GLN THR VAL LYS ALA SEQRES 3 A 316 THR ILE ASP TRP GLU HIS PRO MET PHE LYS LEU TYR GLU SEQRES 4 A 316 LYS ALA LYS ARG ASN GLY LYS TRP ASN PRO ALA ASP ILE SEQRES 5 A 316 ASP PHE SER GLN ASP GLN LYS ASP PHE ALA SER LEU THR SEQRES 6 A 316 SER GLU GLU LYS ILE SER ALA LEU PRO LEU VAL ALA GLY SEQRES 7 A 316 PHE SER ALA GLY ASP GLU ALA VAL THR LEU ASP ILE LEU SEQRES 8 A 316 PRO MET ALA HIS ALA LEU ALA ARG GLN GLY ARG LEU GLU SEQRES 9 A 316 ASP VAL LEU PHE LEU THR THR PHE MET HIS ASP GLU ALA SEQRES 10 A 316 LYS HIS VAL GLU MET PHE SER ARG TRP GLN GLN ALA VAL SEQRES 11 A 316 GLY ILE GLY GLN MET ASP LEU SER VAL PHE HIS ASN ASP SEQRES 12 A 316 HIS TYR LYS ARG ILE PHE TYR GLU ALA LEU PRO GLU ALA SEQRES 13 A 316 MET ASN ARG LEU TYR ALA ASP ASP SER PRO GLU ALA VAL SEQRES 14 A 316 ILE ARG ALA ALA THR VAL TYR ASN MET ILE VAL GLU GLY SEQRES 15 A 316 THR LEU ALA GLU SER GLY TYR TYR THR PHE ARG GLN ILE SEQRES 16 A 316 TYR LYS LYS ALA GLY LEU PHE PRO GLY LEU LEU GLN GLY SEQRES 17 A 316 ILE ASP TYR LEU ASN MET ASP GLU GLY ARG HIS ILE GLN SEQRES 18 A 316 PHE GLY ILE TYR THR ILE GLN ARG ILE VAL ASN GLU ASP SEQRES 19 A 316 GLU ARG TYR TYR GLU LEU PHE ILE ARG TYR MET ASP GLU SEQRES 20 A 316 LEU TRP PRO HIS VAL ILE GLY TYR VAL ASP TYR LEU THR SEQRES 21 A 316 GLU LEU GLY LYS ARG GLN GLN GLN LEU ALA ARG THR TYR SEQRES 22 A 316 ALA LEU GLU ILE ASP TYR ASP LEU LEU ARG HIS TYR VAL SEQRES 23 A 316 ILE LYS GLN PHE ASN LEU ARG LYS LYS GLN ILE SER ARG SEQRES 24 A 316 THR LYS ARG VAL ASP VAL VAL GLU GLY LEU GLU LYS THR SEQRES 25 A 316 ALA ALA GLU SER SEQRES 1 B 316 MET ALA HIS HIS HIS HIS HIS HIS VAL ASP ASP ASP ASP SEQRES 2 B 316 LYS MET VAL HIS HIS ASP GLY PHE GLN THR VAL LYS ALA SEQRES 3 B 316 THR ILE ASP TRP GLU HIS PRO MET PHE LYS LEU TYR GLU SEQRES 4 B 316 LYS ALA LYS ARG ASN GLY LYS TRP ASN PRO ALA ASP ILE SEQRES 5 B 316 ASP PHE SER GLN ASP GLN LYS ASP PHE ALA SER LEU THR SEQRES 6 B 316 SER GLU GLU LYS ILE SER ALA LEU PRO LEU VAL ALA GLY SEQRES 7 B 316 PHE SER ALA GLY ASP GLU ALA VAL THR LEU ASP ILE LEU SEQRES 8 B 316 PRO MET ALA HIS ALA LEU ALA ARG GLN GLY ARG LEU GLU SEQRES 9 B 316 ASP VAL LEU PHE LEU THR THR PHE MET HIS ASP GLU ALA SEQRES 10 B 316 LYS HIS VAL GLU MET PHE SER ARG TRP GLN GLN ALA VAL SEQRES 11 B 316 GLY ILE GLY GLN MET ASP LEU SER VAL PHE HIS ASN ASP SEQRES 12 B 316 HIS TYR LYS ARG ILE PHE TYR GLU ALA LEU PRO GLU ALA SEQRES 13 B 316 MET ASN ARG LEU TYR ALA ASP ASP SER PRO GLU ALA VAL SEQRES 14 B 316 ILE ARG ALA ALA THR VAL TYR ASN MET ILE VAL GLU GLY SEQRES 15 B 316 THR LEU ALA GLU SER GLY TYR TYR THR PHE ARG GLN ILE SEQRES 16 B 316 TYR LYS LYS ALA GLY LEU PHE PRO GLY LEU LEU GLN GLY SEQRES 17 B 316 ILE ASP TYR LEU ASN MET ASP GLU GLY ARG HIS ILE GLN SEQRES 18 B 316 PHE GLY ILE TYR THR ILE GLN ARG ILE VAL ASN GLU ASP SEQRES 19 B 316 GLU ARG TYR TYR GLU LEU PHE ILE ARG TYR MET ASP GLU SEQRES 20 B 316 LEU TRP PRO HIS VAL ILE GLY TYR VAL ASP TYR LEU THR SEQRES 21 B 316 GLU LEU GLY LYS ARG GLN GLN GLN LEU ALA ARG THR TYR SEQRES 22 B 316 ALA LEU GLU ILE ASP TYR ASP LEU LEU ARG HIS TYR VAL SEQRES 23 B 316 ILE LYS GLN PHE ASN LEU ARG LYS LYS GLN ILE SER ARG SEQRES 24 B 316 THR LYS ARG VAL ASP VAL VAL GLU GLY LEU GLU LYS THR SEQRES 25 B 316 ALA ALA GLU SER HET MN A 401 1 HET FE2 A 402 1 HET PLM A 403 49 HET FE2 A 404 1 HET MN B 401 1 HET FE2 B 402 1 HET PLM B 403 49 HET FE2 B 404 1 HETNAM MN MANGANESE (II) ION HETNAM FE2 FE (II) ION HETNAM PLM PALMITIC ACID FORMUL 3 MN 2(MN 2+) FORMUL 4 FE2 4(FE 2+) FORMUL 5 PLM 2(C16 H32 O2) FORMUL 11 HOH *82(H2 O) HELIX 1 AA1 HIS A 18 GLY A 31 1 14 HELIX 2 AA2 ASN A 34 ILE A 38 5 5 HELIX 3 AA3 PHE A 40 SER A 49 1 10 HELIX 4 AA4 ALA A 58 ILE A 76 1 19 HELIX 5 AA5 ILE A 76 GLN A 86 1 11 HELIX 6 AA6 ARG A 88 VAL A 116 1 29 HELIX 7 AA7 ASP A 122 HIS A 127 5 6 HELIX 8 AA8 ASN A 128 TYR A 136 1 9 HELIX 9 AA9 GLU A 137 LEU A 146 1 10 HELIX 10 AB1 SER A 151 ASN A 163 1 13 HELIX 11 AB2 THR A 169 GLY A 186 1 18 HELIX 12 AB3 PHE A 188 ASN A 218 1 31 HELIX 13 AB4 GLU A 221 GLN A 252 1 32 HELIX 14 AB5 GLN A 253 TYR A 259 1 7 HELIX 15 AB6 ASP A 264 GLN A 282 1 19 HELIX 16 AB7 PHE B 7 ALA B 12 1 6 HELIX 17 AB8 HIS B 18 GLY B 31 1 14 HELIX 18 AB9 ASN B 34 ILE B 38 5 5 HELIX 19 AC1 PHE B 40 SER B 49 1 10 HELIX 20 AC2 THR B 51 SER B 66 1 16 HELIX 21 AC3 ILE B 76 GLN B 86 1 11 HELIX 22 AC4 ARG B 88 VAL B 116 1 29 HELIX 23 AC5 ASP B 122 HIS B 127 5 6 HELIX 24 AC6 ASN B 128 TYR B 136 1 9 HELIX 25 AC7 GLU B 137 LEU B 146 1 10 HELIX 26 AC8 SER B 151 ASN B 163 1 13 HELIX 27 AC9 THR B 169 GLY B 186 1 18 HELIX 28 AD1 PHE B 188 ASN B 218 1 31 HELIX 29 AD2 GLU B 221 ARG B 251 1 31 HELIX 30 AD3 ASP B 264 GLN B 282 1 19 LINK OD1 ASP A 69 MN MN A 401 1555 1555 2.16 LINK OE1 GLU A 102 MN MN A 401 1555 1555 2.17 LINK OE2 GLU A 102 FE FE2 A 402 1555 1555 2.19 LINK ND1 HIS A 105 MN MN A 401 1555 1555 2.24 LINK NE2 HIS A 130 FE FE2 A 404 1555 1555 2.35 LINK OE2 GLU A 167 FE FE2 A 402 1555 1555 1.99 LINK OE2 GLU A 202 MN MN A 401 1555 1555 2.40 LINK OE1 GLU A 202 FE FE2 A 402 1555 1555 2.48 LINK OE2 GLU A 202 FE FE2 A 402 1555 1555 2.16 LINK ND1 HIS A 205 FE FE2 A 402 1555 1555 2.43 LINK MN MN A 401 O2 PLM A 403 1555 1555 2.03 LINK MN MN A 401 O HOH A 503 1555 1555 2.95 LINK FE FE2 A 402 O1 PLM A 403 1555 1555 2.26 LINK OE1 GLU B 102 MN MN B 401 1555 1555 2.17 LINK OE2 GLU B 102 MN MN B 401 1555 1555 2.34 LINK OE2 GLU B 102 FE FE2 B 402 1555 1555 2.23 LINK ND1 HIS B 105 MN MN B 401 1555 1555 2.20 LINK NE2 HIS B 130 FE FE2 B 404 1555 1555 2.19 LINK OE2 GLU B 167 FE FE2 B 402 1555 1555 1.80 LINK OE2 GLU B 202 MN MN B 401 1555 1555 2.21 LINK OE1 GLU B 202 FE FE2 B 402 1555 1555 2.19 LINK OE2 GLU B 202 FE FE2 B 402 1555 1555 2.53 LINK ND1 HIS B 205 FE FE2 B 402 1555 1555 2.60 LINK FE FE2 B 404 O HOH B 532 1555 1555 2.58 SITE 1 AC1 7 ASP A 69 GLU A 102 HIS A 105 GLU A 202 SITE 2 AC1 7 FE2 A 402 PLM A 403 HOH A 503 SITE 1 AC2 6 GLU A 102 GLU A 167 GLU A 202 HIS A 205 SITE 2 AC2 6 MN A 401 PLM A 403 SITE 1 AC3 12 LEU A 61 GLY A 64 PHE A 65 ASP A 69 SITE 2 AC3 12 VAL A 72 GLU A 102 VAL A 166 GLU A 167 SITE 3 AC3 12 LEU A 170 GLU A 202 MN A 401 FE2 A 402 SITE 1 AC4 1 HIS A 130 SITE 1 AC5 4 GLU B 102 HIS B 105 GLU B 202 FE2 B 402 SITE 1 AC6 5 GLU B 102 GLU B 167 GLU B 202 HIS B 205 SITE 2 AC6 5 MN B 401 SITE 1 AC7 8 LEU B 61 GLY B 64 PHE B 65 ALA B 67 SITE 2 AC7 8 LEU B 170 GLY B 174 THR B 177 TYR B 265 SITE 1 AC8 3 ASP B 129 HIS B 130 HOH B 532 CRYST1 160.808 55.963 98.059 90.00 126.23 90.00 C 1 2 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006219 0.000000 0.004556 0.00000 SCALE2 0.000000 0.017869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012642 0.00000