HEADER TRANSFERASE 16-MAY-17 5O0I TITLE ADP-DEPENDENT GLUCOKINASE FROM PYROCOCCUS HORIKOSHII COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-DEPENDENT GLUCOKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADPGK; COMPND 5 EC: 2.7.1.147; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII (STRAIN ATCC 700860 / DSM SOURCE 3 12428 / JCM 9974 / NBRC 100139 / OT-3); SOURCE 4 ORGANISM_TAXID: 70601; SOURCE 5 STRAIN: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3; SOURCE 6 GENE: GLKA, PH0589; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADP-DEPENDENT GLUCOKINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.GRUDNIK,G.DUBIN REVDAT 4 17-JAN-24 5O0I 1 REMARK REVDAT 3 25-JUL-18 5O0I 1 JRNL REVDAT 2 27-JUN-18 5O0I 1 JRNL ATOM REVDAT 1 30-MAY-18 5O0I 0 JRNL AUTH P.GRUDNIK,M.M.KAMINSKI,K.P.REMBACZ,K.KUSKA,M.MADEJ, JRNL AUTH 2 J.POTEMPA,M.DAWIDOWSKI,G.DUBIN JRNL TITL STRUCTURAL BASIS FOR ADP-DEPENDENT GLUCOKINASE INHIBITION BY JRNL TITL 2 8-BROMO-SUBSTITUTED ADENOSINE NUCLEOTIDE. JRNL REF J. BIOL. CHEM. V. 293 11088 2018 JRNL REFN ESSN 1083-351X JRNL PMID 29784881 JRNL DOI 10.1074/JBC.RA117.001562 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1567 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 44.6408 - 4.4469 1.00 2922 160 0.1855 0.2263 REMARK 3 2 4.4469 - 3.5301 1.00 2810 135 0.1401 0.1877 REMARK 3 3 3.5301 - 3.0840 1.00 2724 174 0.1428 0.1888 REMARK 3 4 3.0840 - 2.8020 1.00 2779 129 0.1573 0.1735 REMARK 3 5 2.8020 - 2.6012 1.00 2733 145 0.1543 0.2171 REMARK 3 6 2.6012 - 2.4479 1.00 2742 132 0.1681 0.2607 REMARK 3 7 2.4479 - 2.3253 1.00 2725 131 0.1641 0.2229 REMARK 3 8 2.3253 - 2.2241 1.00 2726 133 0.1837 0.2553 REMARK 3 9 2.2241 - 2.1385 1.00 2685 160 0.2016 0.2352 REMARK 3 10 2.1385 - 2.0647 1.00 2693 146 0.2162 0.3072 REMARK 3 11 2.0647 - 2.0001 1.00 2719 122 0.2459 0.2949 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.97 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 : 0.012 3670 REMARK 3 ANGLE : 1.146 4964 REMARK 3 CHIRALITY : 0.062 559 REMARK 3 PLANARITY : 0.008 627 REMARK 3 DIHEDRAL : 20.698 2200 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): 38.1412 -25.4333 -20.6371 REMARK 3 T TENSOR REMARK 3 T11: 0.1552 T22: 0.1938 REMARK 3 T33: 0.0902 T12: 0.0049 REMARK 3 T13: -0.0808 T23: 0.0286 REMARK 3 L TENSOR REMARK 3 L11: 0.9408 L22: 2.1014 REMARK 3 L33: 0.6206 L12: -0.1189 REMARK 3 L13: -0.8551 L23: 0.4913 REMARK 3 S TENSOR REMARK 3 S11: -0.0595 S12: -0.1202 S13: -0.1076 REMARK 3 S21: -0.0562 S22: 0.0692 S23: -0.0883 REMARK 3 S31: 0.0079 S32: 0.0419 S33: -0.0682 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 44 THROUGH 106 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.1979 -1.0289 -12.5535 REMARK 3 T TENSOR REMARK 3 T11: 0.1618 T22: 0.2692 REMARK 3 T33: 0.3297 T12: 0.0318 REMARK 3 T13: -0.0376 T23: 0.0850 REMARK 3 L TENSOR REMARK 3 L11: 3.5211 L22: 3.6285 REMARK 3 L33: 3.0357 L12: -0.0108 REMARK 3 L13: -0.2022 L23: -0.0623 REMARK 3 S TENSOR REMARK 3 S11: 0.0533 S12: 0.0019 S13: 0.1064 REMARK 3 S21: -0.1512 S22: 0.1616 S23: 0.8100 REMARK 3 S31: -0.1646 S32: -0.4961 S33: -0.0212 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 107 THROUGH 169 ) REMARK 3 ORIGIN FOR THE GROUP (A): 43.3857 -11.1801 -13.2094 REMARK 3 T TENSOR REMARK 3 T11: 0.1849 T22: 0.2395 REMARK 3 T33: 0.1449 T12: -0.0148 REMARK 3 T13: -0.0328 T23: -0.0434 REMARK 3 L TENSOR REMARK 3 L11: 1.9813 L22: 1.6001 REMARK 3 L33: 1.8132 L12: -1.3347 REMARK 3 L13: -0.8392 L23: 0.1932 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.3931 S13: 0.1470 REMARK 3 S21: 0.1654 S22: 0.0798 S23: -0.2171 REMARK 3 S31: 0.0212 S32: 0.2826 S33: -0.0842 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 170 THROUGH 211 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0567 -7.9160 -13.5616 REMARK 3 T TENSOR REMARK 3 T11: 0.2179 T22: 0.1799 REMARK 3 T33: 0.2499 T12: -0.0236 REMARK 3 T13: -0.0648 T23: 0.0710 REMARK 3 L TENSOR REMARK 3 L11: 4.2924 L22: 2.5526 REMARK 3 L33: 2.3546 L12: -0.3747 REMARK 3 L13: -0.9665 L23: 0.3541 REMARK 3 S TENSOR REMARK 3 S11: 0.2592 S12: -0.0989 S13: -0.2611 REMARK 3 S21: -0.0647 S22: 0.1160 S23: 0.3701 REMARK 3 S31: 0.1225 S32: -0.2401 S33: -0.0564 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 212 THROUGH 234 ) REMARK 3 ORIGIN FOR THE GROUP (A): 49.0262 -5.0077 -24.9596 REMARK 3 T TENSOR REMARK 3 T11: 0.1699 T22: 0.1614 REMARK 3 T33: 0.1778 T12: -0.0264 REMARK 3 T13: 0.0334 T23: -0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.6783 L22: 4.1347 REMARK 3 L33: 2.2777 L12: -1.0915 REMARK 3 L13: -1.0807 L23: 0.9954 REMARK 3 S TENSOR REMARK 3 S11: 0.2339 S12: -0.0208 S13: 0.4504 REMARK 3 S21: -0.0178 S22: -0.0215 S23: -0.4988 REMARK 3 S31: -0.1776 S32: 0.3216 S33: -0.2546 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 235 THROUGH 305 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.4924 -8.3603 -34.7605 REMARK 3 T TENSOR REMARK 3 T11: 0.2385 T22: 0.1954 REMARK 3 T33: 0.1477 T12: 0.0317 REMARK 3 T13: 0.0049 T23: 0.0396 REMARK 3 L TENSOR REMARK 3 L11: 3.2645 L22: 1.5885 REMARK 3 L33: 1.0470 L12: -0.0392 REMARK 3 L13: 0.0680 L23: 0.4929 REMARK 3 S TENSOR REMARK 3 S11: -0.0565 S12: 0.2789 S13: 0.2416 REMARK 3 S21: -0.2517 S22: 0.0553 S23: 0.1097 REMARK 3 S31: -0.2747 S32: -0.1127 S33: -0.1155 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 306 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.1727 -23.3457 -39.6440 REMARK 3 T TENSOR REMARK 3 T11: 0.1948 T22: 0.2334 REMARK 3 T33: 0.1262 T12: 0.0028 REMARK 3 T13: -0.0125 T23: -0.0222 REMARK 3 L TENSOR REMARK 3 L11: 3.0757 L22: 4.3705 REMARK 3 L33: 4.9039 L12: 0.1259 REMARK 3 L13: 0.9111 L23: -1.1471 REMARK 3 S TENSOR REMARK 3 S11: -0.1053 S12: 0.3213 S13: 0.0801 REMARK 3 S21: -0.2525 S22: 0.1143 S23: 0.3495 REMARK 3 S31: -0.2045 S32: -0.3453 S33: -0.0067 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 457 ) REMARK 3 ORIGIN FOR THE GROUP (A): 33.4770 -31.5036 -28.3375 REMARK 3 T TENSOR REMARK 3 T11: 0.1329 T22: 0.1657 REMARK 3 T33: 0.1441 T12: 0.0126 REMARK 3 T13: 0.0199 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 2.7662 L22: 2.6902 REMARK 3 L33: 3.4600 L12: 1.4021 REMARK 3 L13: 0.8337 L23: -0.0243 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: -0.2188 S13: 0.0040 REMARK 3 S21: 0.1185 S22: -0.1008 S23: 0.0062 REMARK 3 S31: 0.2295 S32: -0.2291 S33: -0.0109 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 5O0I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004994. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-16 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31825 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.78 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 20.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1L2L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (W/V) PEG 6000, 0.2 M LISO4, AND REMARK 280 0.1 M CITRATE BUFFER (PH 3.6), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 89.25933 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 44.62967 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 0.00000 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 44.62967 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 89.25933 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 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 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 738 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 PRO A 435 REMARK 465 LYS A 436 REMARK 465 SER A 437 REMARK 465 THR A 438 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 4 CG SD CE REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 161 CG CD OE1 OE2 REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 189 CG CD CE NZ REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 GLU A 243 CG CD OE1 OE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 SER A 317 OG REMARK 470 LYS A 318 CG CD CE NZ REMARK 470 ASP A 319 CG OD1 OD2 REMARK 470 ASN A 380 CG OD1 ND2 REMARK 470 GLU A 382 CG CD OE1 OE2 REMARK 470 LYS A 433 CG CD CE NZ REMARK 470 LYS A 434 CG CD CE NZ REMARK 470 HIS A 457 CG ND1 CD2 CE1 NE2 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 HH TYR A 32 HD1 HIS A 255 1.24 REMARK 500 HG SER A 385 O HOH A 605 1.45 REMARK 500 HH22 ARG A 253 O HOH A 601 1.46 REMARK 500 HE ARG A 168 O HOH A 603 1.49 REMARK 500 HH21 ARG A 265 O2 EDO A 509 1.49 REMARK 500 HE ARG A 163 O HOH A 606 1.53 REMARK 500 HE ARG A 104 O3 SO4 A 507 1.57 REMARK 500 HZ3 LYS A 43 O HOH A 607 1.58 REMARK 500 HH12 ARG A 253 O HOH A 601 1.59 REMARK 500 O HOH A 750 O HOH A 763 1.83 REMARK 500 O HOH A 741 O HOH A 759 1.84 REMARK 500 O HOH A 633 O HOH A 651 1.96 REMARK 500 O HOH A 717 O HOH A 765 1.97 REMARK 500 O HOH A 748 O HOH A 756 1.98 REMARK 500 NH2 ARG A 253 O HOH A 601 2.15 REMARK 500 O HOH A 623 O HOH A 732 2.18 REMARK 500 NZ LYS A 332 OE1 GLU A 336 2.19 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 NH1 ARG A 26 OD1 ASP A 207 6654 2.12 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 SER A 411 C - N - CA ANGL. DEV. = -15.4 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 GLU A 158 -99.40 -95.14 REMARK 500 LEU A 191 -108.48 50.64 REMARK 500 ASN A 199 -159.23 -168.05 REMARK 500 GLU A 308 66.87 -107.10 REMARK 500 ASP A 322 102.96 -44.40 REMARK 500 GLU A 420 -131.67 53.62 REMARK 500 LYS A 433 73.50 66.03 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 SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 510 DBREF 5O0I A 4 457 UNP O58328 GLKA_PYRHO 4 457 SEQRES 1 A 454 MET THR ASN TRP GLU SER LEU TYR GLU LYS ALA LEU ASP SEQRES 2 A 454 LYS VAL GLU ALA SER ILE ARG LYS VAL ARG GLY VAL LEU SEQRES 3 A 454 LEU ALA TYR ASN THR ASN ILE ASP ALA ILE LYS TYR LEU SEQRES 4 A 454 LYS ARG GLU ASP LEU GLU LYS ARG ILE GLU LYS VAL GLY SEQRES 5 A 454 LYS GLU GLU VAL LEU ARG TYR SER GLU GLU LEU PRO LYS SEQRES 6 A 454 GLU ILE GLU THR ILE PRO GLN LEU LEU GLY SER ILE LEU SEQRES 7 A 454 TRP SER ILE LYS ARG GLY LYS ALA ALA GLU LEU LEU VAL SEQRES 8 A 454 VAL SER ARG GLU VAL ARG GLU TYR MET ARG LYS TRP GLY SEQRES 9 A 454 TRP ASP GLU LEU ARG MET GLY GLY GLN VAL GLY ILE MET SEQRES 10 A 454 ALA ASN LEU LEU GLY GLY VAL TYR GLY ILE PRO VAL ILE SEQRES 11 A 454 ALA HIS VAL PRO GLN LEU SER GLU LEU GLN ALA SER LEU SEQRES 12 A 454 PHE LEU ASP GLY PRO ILE TYR VAL PRO THR PHE GLU ARG SEQRES 13 A 454 GLY GLU LEU ARG LEU ILE HIS PRO ARG GLU PHE ARG LYS SEQRES 14 A 454 GLY GLU GLU ASP CYS ILE HIS TYR ILE TYR GLU PHE PRO SEQRES 15 A 454 ARG ASN PHE LYS VAL LEU ASP PHE GLU ALA PRO ARG GLU SEQRES 16 A 454 ASN ARG PHE ILE GLY ALA ALA ASP ASP TYR ASN PRO ILE SEQRES 17 A 454 LEU TYR VAL ARG GLU GLU TRP ILE GLU ARG PHE GLU GLU SEQRES 18 A 454 ILE ALA LYS ARG SER GLU LEU ALA ILE ILE SER GLY LEU SEQRES 19 A 454 HIS PRO LEU THR GLN GLU ASN HIS GLY LYS PRO ILE LYS SEQRES 20 A 454 LEU VAL ARG GLU HIS LEU LYS ILE LEU ASN ASP LEU GLY SEQRES 21 A 454 ILE ARG ALA HIS LEU GLU PHE ALA PHE THR PRO ASP GLU SEQRES 22 A 454 VAL VAL ARG LEU GLU ILE VAL LYS LEU LEU LYS HIS PHE SEQRES 23 A 454 TYR SER VAL GLY LEU ASN GLU VAL GLU LEU ALA SER VAL SEQRES 24 A 454 VAL SER VAL MET GLY GLU LYS GLU LEU ALA GLU ARG ILE SEQRES 25 A 454 ILE SER LYS ASP PRO ALA ASP PRO ILE ALA VAL ILE GLU SEQRES 26 A 454 GLY LEU LEU LYS LEU ILE LYS GLU THR GLY VAL LYS ARG SEQRES 27 A 454 ILE HIS PHE HIS THR TYR GLY TYR TYR LEU ALA LEU THR SEQRES 28 A 454 ARG GLU LYS GLY GLU HIS VAL ARG ASP ALA LEU LEU PHE SEQRES 29 A 454 SER ALA LEU ALA ALA ALA THR LYS ALA MET LYS GLY ASN SEQRES 30 A 454 ILE GLU LYS LEU SER ASP ILE ARG GLU GLY LEU ALA VAL SEQRES 31 A 454 PRO ILE GLY GLU GLN GLY LEU GLU VAL GLU LYS ILE LEU SEQRES 32 A 454 GLU LYS GLU PHE SER LEU ARG ASP GLY ILE GLY SER ILE SEQRES 33 A 454 GLU ASP TYR GLN LEU THR PHE ILE PRO THR LYS VAL VAL SEQRES 34 A 454 LYS LYS PRO LYS SER THR VAL GLY ILE GLY ASP THR ILE SEQRES 35 A 454 SER SER SER ALA PHE VAL SER GLU PHE SER LEU HIS HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET EDO A 508 10 HET EDO A 509 10 HET ACT A 510 7 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SO4 7(O4 S 2-) FORMUL 9 EDO 2(C2 H6 O2) FORMUL 11 ACT C2 H3 O2 1- FORMUL 12 HOH *170(H2 O) HELIX 1 AA1 ASN A 6 ILE A 22 1 17 HELIX 2 AA2 ARG A 23 VAL A 25 5 3 HELIX 3 AA3 LYS A 43 GLY A 55 1 13 HELIX 4 AA4 GLY A 55 GLU A 65 1 11 HELIX 5 AA5 THR A 72 GLY A 87 1 16 HELIX 6 AA6 SER A 96 GLY A 107 1 12 HELIX 7 AA7 GLY A 115 GLY A 125 1 11 HELIX 8 AA8 SER A 140 LEU A 146 1 7 HELIX 9 AA9 HIS A 166 PHE A 170 5 5 HELIX 10 AB1 TYR A 208 LEU A 212 5 5 HELIX 11 AB2 ARG A 215 ARG A 221 1 7 HELIX 12 AB3 ARG A 221 LYS A 227 1 7 HELIX 13 AB4 HIS A 245 GLY A 263 1 19 HELIX 14 AB5 ASP A 275 LEU A 286 1 12 HELIX 15 AB6 LYS A 287 PHE A 289 5 3 HELIX 16 AB7 ASN A 295 MET A 306 1 12 HELIX 17 AB8 GLU A 308 LYS A 318 1 11 HELIX 18 AB9 ASP A 322 GLY A 338 1 17 HELIX 19 AC1 GLY A 358 GLY A 379 1 22 HELIX 20 AC2 LYS A 383 VAL A 393 5 11 HELIX 21 AC3 GLY A 396 PHE A 410 1 15 HELIX 22 AC4 GLY A 440 HIS A 457 1 18 SHEET 1 AA111 LEU A 162 ILE A 165 0 SHEET 2 AA111 ILE A 152 PHE A 157 -1 N THR A 156 O ARG A 163 SHEET 3 AA111 VAL A 132 ALA A 134 1 N ALA A 134 O TYR A 153 SHEET 4 AA111 VAL A 28 ALA A 31 1 N LEU A 30 O ILE A 133 SHEET 5 AA111 LEU A 231 ILE A 234 1 O LEU A 231 N LEU A 29 SHEET 6 AA111 ARG A 265 GLU A 269 1 O HIS A 267 N ILE A 234 SHEET 7 AA111 SER A 291 LEU A 294 1 O GLY A 293 N LEU A 268 SHEET 8 AA111 ARG A 341 HIS A 345 1 O HIS A 343 N VAL A 292 SHEET 9 AA111 TYR A 349 THR A 354 -1 O LEU A 351 N PHE A 344 SHEET 10 AA111 TYR A 422 PRO A 428 -1 O THR A 425 N ALA A 352 SHEET 11 AA111 ILE A 416 ILE A 419 -1 N GLY A 417 O LEU A 424 SHEET 1 AA2 5 ALA A 90 LEU A 93 0 SHEET 2 AA2 5 ASN A 199 ALA A 205 1 O ALA A 204 N LEU A 92 SHEET 3 AA2 5 ILE A 178 PHE A 184 -1 N TYR A 182 O PHE A 201 SHEET 4 AA2 5 ASN A 35 TYR A 41 1 N ALA A 38 O ILE A 181 SHEET 5 AA2 5 GLU A 110 GLY A 114 -1 O GLU A 110 N ILE A 39 SHEET 1 AA3 2 LYS A 189 VAL A 190 0 SHEET 2 AA3 2 PHE A 193 GLU A 194 -1 O PHE A 193 N VAL A 190 CISPEP 1 ALA A 31 TYR A 32 0 12.11 CISPEP 2 ASP A 319 PRO A 320 0 5.08 SITE 1 AC1 6 ASP A 149 GLY A 150 HIS A 166 ARG A 168 SITE 2 AC1 6 LYS A 332 GLU A 336 SITE 1 AC2 4 LYS A 430 VAL A 431 VAL A 432 LYS A 433 SITE 1 AC3 4 LYS A 88 ALA A 89 ARG A 197 ASN A 199 SITE 1 AC4 7 ASN A 33 GLN A 116 HIS A 238 HOH A 602 SITE 2 AC4 7 HOH A 633 HOH A 648 HOH A 670 SITE 1 AC5 3 GLY A 358 GLU A 359 HIS A 360 SITE 1 AC6 8 ARG A 100 ASP A 176 CYS A 177 ALA A 205 SITE 2 AC6 8 ASP A 206 ASP A 207 TYR A 208 HOH A 650 SITE 1 AC7 2 ARG A 100 ARG A 104 SITE 1 AC8 3 ARG A 186 ARG A 197 GLU A 198 SITE 1 AC9 4 ARG A 265 TYR A 290 LYS A 340 HOH A 723 SITE 1 AD1 4 ASN A 295 GLU A 296 THR A 346 TYR A 347 CRYST1 77.135 77.135 133.889 90.00 90.00 120.00 P 32 2 1 6 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 0.012964 0.007485 0.000000 0.00000 SCALE2 0.000000 0.014970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007469 0.00000