HEADER HYDROLASE 31-MAR-14 4PZZ TITLE SECOND-SITE SCREENING OF K-RAS IN THE PRESENCE OF COVALENTLY ATTACHED TITLE 2 FIRST-SITE LIGANDS COMPND MOL_ID: 1; COMPND 2 MOLECULE: K-RAS; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.5.2; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SMALL GTPASE, SIGNALING TRANSDUCTION, SOS, RAF, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.SUN,J.PHAN,A.FRIBERG,D.V.CAMPER,E.T.OLEJNICZAK,S.W.FESIK REVDAT 2 20-NOV-24 4PZZ 1 REMARK SEQADV LINK REVDAT 1 10-SEP-14 4PZZ 0 JRNL AUTH Q.SUN,J.PHAN,A.R.FRIBERG,D.V.CAMPER,E.T.OLEJNICZAK,S.W.FESIK JRNL TITL A METHOD FOR THE SECOND-SITE SCREENING OF K-RAS IN THE JRNL TITL 2 PRESENCE OF A COVALENTLY ATTACHED FIRST-SITE LIGAND. JRNL REF J.BIOMOL.NMR V. 60 11 2014 JRNL REFN ISSN 0925-2738 JRNL PMID 25087006 JRNL DOI 10.1007/S10858-014-9849-8 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 28456 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1431 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 28.3130 - 3.0209 1.00 3011 148 0.1282 0.1402 REMARK 3 2 3.0209 - 2.3982 1.00 2851 154 0.1360 0.1576 REMARK 3 3 2.3982 - 2.0952 1.00 2852 138 0.1204 0.1523 REMARK 3 4 2.0952 - 1.9036 1.00 2821 150 0.1261 0.1499 REMARK 3 5 1.9036 - 1.7672 1.00 2783 136 0.1318 0.1675 REMARK 3 6 1.7672 - 1.6630 1.00 2798 143 0.1350 0.1707 REMARK 3 7 1.6630 - 1.5798 1.00 2784 135 0.1303 0.1853 REMARK 3 8 1.5798 - 1.5110 1.00 2767 157 0.1372 0.1671 REMARK 3 9 1.5110 - 1.4528 0.85 2327 138 0.1426 0.1656 REMARK 3 10 1.4528 - 1.4027 0.74 2031 132 0.1526 0.1842 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.010 1422 REMARK 3 ANGLE : 1.385 1925 REMARK 3 CHIRALITY : 0.074 213 REMARK 3 PLANARITY : 0.006 246 REMARK 3 DIHEDRAL : 16.456 535 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 4PZZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.403 REMARK 200 RESOLUTION RANGE LOW (A) : 28.307 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.3 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 4000, 0.1 M MMT PH 4.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.53800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.83900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.53150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.83900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.53800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.53150 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 37 HE2 GLU A 62 1.58 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 117 35.77 78.47 REMARK 500 ARG A 149 -1.05 80.51 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 GDP A 201 O3B 91.2 REMARK 620 3 HOH A 302 O 84.0 95.1 REMARK 620 4 HOH A 304 O 90.4 85.5 174.4 REMARK 620 5 HOH A 305 O 90.5 169.6 95.3 84.2 REMARK 620 6 HOH A 309 O 173.5 89.2 89.5 96.0 90.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2XO A 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PZY RELATED DB: PDB REMARK 900 RELATED ID: 4Q01 RELATED DB: PDB REMARK 900 RELATED ID: 4Q02 RELATED DB: PDB REMARK 900 RELATED ID: 4Q03 RELATED DB: PDB DBREF 4PZZ A 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 4PZZ GLY A 0 UNP P01116 EXPRESSION TAG SEQADV 4PZZ VAL A 12 UNP P01116 GLY 12 ENGINEERED MUTATION SEQADV 4PZZ CYS A 39 UNP P01116 SER 39 ENGINEERED MUTATION SEQADV 4PZZ SER A 118 UNP P01116 CYS 118 ENGINEERED MUTATION SEQRES 1 A 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA VAL SEQRES 2 A 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 A 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 170 CYS TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 A 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 A 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 A 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 A 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 A 170 LYS SER ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 A 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 A 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 A 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 A 170 LYS HET GDP A 201 38 HET MG A 202 1 HET 2XO A 203 11 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM 2XO 1H-BENZIMIDAZOL-2-YLMETHANETHIOL FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ FORMUL 4 2XO C8 H8 N2 S FORMUL 5 HOH *304(H2 O) HELIX 1 1 GLY A 15 ASN A 26 1 12 HELIX 2 2 TYR A 64 GLY A 75 1 12 HELIX 3 3 ASN A 86 ASP A 92 1 7 HELIX 4 4 ASP A 92 ASP A 105 1 14 HELIX 5 5 ASP A 126 GLY A 138 1 13 HELIX 6 6 GLY A 151 GLU A 168 1 18 SHEET 1 A 6 ASP A 38 ILE A 46 0 SHEET 2 A 6 GLU A 49 ASP A 57 -1 O LEU A 53 N LYS A 42 SHEET 3 A 6 GLU A 3 VAL A 9 1 N TYR A 4 O LEU A 52 SHEET 4 A 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 9 SHEET 5 A 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 A 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 LINK SG CYS A 39 SAH 2XO A 203 1555 1555 2.07 LINK OG SER A 17 MG MG A 202 1555 1555 2.17 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.05 LINK MG MG A 202 O HOH A 302 1555 1555 2.09 LINK MG MG A 202 O HOH A 304 1555 1555 2.10 LINK MG MG A 202 O HOH A 305 1555 1555 2.09 LINK MG MG A 202 O HOH A 309 1555 1555 2.06 SITE 1 AC1 26 GLY A 13 VAL A 14 GLY A 15 LYS A 16 SITE 2 AC1 26 SER A 17 ALA A 18 PHE A 28 ASP A 30 SITE 3 AC1 26 TYR A 32 ASN A 116 LYS A 117 ASP A 119 SITE 4 AC1 26 LEU A 120 SER A 145 ALA A 146 LYS A 147 SITE 5 AC1 26 MG A 202 HOH A 302 HOH A 304 HOH A 309 SITE 6 AC1 26 HOH A 321 HOH A 349 HOH A 431 HOH A 450 SITE 7 AC1 26 HOH A 505 HOH A 579 SITE 1 AC2 6 SER A 17 GDP A 201 HOH A 302 HOH A 304 SITE 2 AC2 6 HOH A 305 HOH A 309 SITE 1 AC3 5 VAL A 7 CYS A 39 ASP A 54 TYR A 71 SITE 2 AC3 5 HOH A 401 CRYST1 39.076 41.063 91.678 90.00 90.00 90.00 P 21 21 21 4 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 0.025591 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010908 0.00000