HEADER TRANSFERASE 17-FEB-15 4YAP TITLE CRYSTAL STRUCTURE OF LIGG-APO FORM FROM SPHINGOBIUM SP. STRAIN SYK-6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTATHIONE S-TRANSFERASE HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOBIUM SP. SYK-6; SOURCE 3 ORGANISM_TAXID: 627192; SOURCE 4 GENE: LIGG; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GSH-LYASE GSH-DEPENDENT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.H.PEREIRA,R.P.MCANDREW,R.A.HEINS,K.L.SALE,B.A.SIMMONS,P.D.ADAMS REVDAT 4 28-FEB-24 4YAP 1 JRNL REMARK REVDAT 3 01-JUN-16 4YAP 1 JRNL REVDAT 2 16-MAR-16 4YAP 1 JRNL REVDAT 1 09-MAR-16 4YAP 0 JRNL AUTH J.H.PEREIRA,R.A.HEINS,D.L.GALL,R.P.MCANDREW,K.DENG, JRNL AUTH 2 K.C.HOLLAND,T.J.DONOHUE,D.R.NOGUERA,B.A.SIMMONS,K.L.SALE, JRNL AUTH 3 J.RALPH,P.D.ADAMS JRNL TITL STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF THE EARLY AND JRNL TITL 2 LATE ENZYMES IN THE LIGNIN BETA-ARYL ETHER CLEAVAGE PATHWAY JRNL TITL 3 FROM SPHINGOBIUM SP. SYK-6. JRNL REF J.BIOL.CHEM. V. 291 10228 2016 JRNL REFN ESSN 1083-351X JRNL PMID 26940872 JRNL DOI 10.1074/JBC.M115.700427 REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1839 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 115285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 5784 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 41.0829 - 3.4520 0.97 3808 198 0.1625 0.1579 REMARK 3 2 3.4520 - 2.7401 1.00 3746 209 0.1606 0.1760 REMARK 3 3 2.7401 - 2.3938 1.00 3729 193 0.1601 0.1826 REMARK 3 4 2.3938 - 2.1749 1.00 3686 221 0.1491 0.1709 REMARK 3 5 2.1749 - 2.0191 1.00 3684 186 0.1536 0.1777 REMARK 3 6 2.0191 - 1.9000 1.00 3702 181 0.1577 0.1774 REMARK 3 7 1.9000 - 1.8049 1.00 3661 186 0.1601 0.1718 REMARK 3 8 1.8049 - 1.7263 1.00 3724 170 0.1647 0.1866 REMARK 3 9 1.7263 - 1.6598 1.00 3661 183 0.1576 0.1802 REMARK 3 10 1.6598 - 1.6026 1.00 3663 188 0.1604 0.1591 REMARK 3 11 1.6026 - 1.5524 1.00 3610 216 0.1610 0.1715 REMARK 3 12 1.5524 - 1.5081 1.00 3655 204 0.1658 0.1928 REMARK 3 13 1.5081 - 1.4684 1.00 3609 199 0.1743 0.2001 REMARK 3 14 1.4684 - 1.4325 1.00 3666 194 0.1733 0.1752 REMARK 3 15 1.4325 - 1.4000 1.00 3620 191 0.1762 0.1948 REMARK 3 16 1.4000 - 1.3702 1.00 3610 199 0.1779 0.2135 REMARK 3 17 1.3702 - 1.3428 1.00 3654 192 0.1832 0.2179 REMARK 3 18 1.3428 - 1.3174 1.00 3604 179 0.1847 0.2006 REMARK 3 19 1.3174 - 1.2939 1.00 3658 177 0.1868 0.2088 REMARK 3 20 1.2939 - 1.2720 1.00 3651 205 0.1876 0.2074 REMARK 3 21 1.2720 - 1.2514 1.00 3627 201 0.1855 0.2231 REMARK 3 22 1.2514 - 1.2322 1.00 3590 195 0.1988 0.1964 REMARK 3 23 1.2322 - 1.2141 1.00 3618 199 0.1968 0.2097 REMARK 3 24 1.2141 - 1.1970 1.00 3620 188 0.1914 0.1799 REMARK 3 25 1.1970 - 1.1808 1.00 3621 186 0.1985 0.2127 REMARK 3 26 1.1808 - 1.1654 1.00 3627 203 0.2052 0.2237 REMARK 3 27 1.1654 - 1.1509 1.00 3578 182 0.2144 0.2271 REMARK 3 28 1.1509 - 1.1370 1.00 3648 174 0.2284 0.2440 REMARK 3 29 1.1370 - 1.1238 1.00 3630 197 0.2474 0.2696 REMARK 3 30 1.1238 - 1.1112 0.99 3541 188 0.2660 0.2720 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.630 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 : 0.019 2258 REMARK 3 ANGLE : 1.837 3062 REMARK 3 CHIRALITY : 0.103 311 REMARK 3 PLANARITY : 0.014 403 REMARK 3 DIHEDRAL : 12.947 856 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 48 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.3930 54.2208 0.3615 REMARK 3 T TENSOR REMARK 3 T11: 0.1166 T22: 0.1112 REMARK 3 T33: 0.0816 T12: 0.0236 REMARK 3 T13: -0.0060 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 1.2056 L22: 1.4032 REMARK 3 L33: 1.2734 L12: 0.7118 REMARK 3 L13: -0.5640 L23: -0.3366 REMARK 3 S TENSOR REMARK 3 S11: -0.0591 S12: 0.1927 S13: 0.0660 REMARK 3 S21: -0.1557 S22: 0.0385 S23: -0.0351 REMARK 3 S31: -0.0669 S32: -0.0741 S33: 0.0090 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 49 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1551 63.2806 5.7921 REMARK 3 T TENSOR REMARK 3 T11: 0.1428 T22: 0.1128 REMARK 3 T33: 0.0849 T12: 0.0563 REMARK 3 T13: -0.0065 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.9934 L22: 5.7623 REMARK 3 L33: 3.7484 L12: 0.1768 REMARK 3 L13: -1.9138 L23: -0.3385 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: 0.0278 S13: 0.1531 REMARK 3 S21: 0.0465 S22: 0.0297 S23: -0.1438 REMARK 3 S31: -0.1685 S32: 0.0964 S33: 0.0629 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 117 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.2979 49.2572 17.1480 REMARK 3 T TENSOR REMARK 3 T11: 0.0941 T22: 0.0576 REMARK 3 T33: 0.0711 T12: -0.0030 REMARK 3 T13: -0.0063 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.8470 L22: 0.3388 REMARK 3 L33: 1.0749 L12: -0.0546 REMARK 3 L13: -0.6666 L23: 0.0368 REMARK 3 S TENSOR REMARK 3 S11: 0.0842 S12: 0.0365 S13: -0.0145 REMARK 3 S21: -0.0131 S22: -0.0340 S23: 0.0563 REMARK 3 S31: -0.0727 S32: -0.1259 S33: -0.0534 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 118 THROUGH 145 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.0358 39.0640 21.7193 REMARK 3 T TENSOR REMARK 3 T11: 0.0777 T22: 0.1002 REMARK 3 T33: 0.0704 T12: -0.0006 REMARK 3 T13: -0.0169 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 4.7708 L22: 0.9056 REMARK 3 L33: 1.9828 L12: 0.5349 REMARK 3 L13: -1.7310 L23: -0.6209 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: -0.2047 S13: 0.0055 REMARK 3 S21: 0.0103 S22: -0.0156 S23: -0.0993 REMARK 3 S31: 0.0155 S32: 0.3104 S33: -0.0030 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 146 THROUGH 219 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.7136 38.1789 11.5801 REMARK 3 T TENSOR REMARK 3 T11: 0.0869 T22: 0.0476 REMARK 3 T33: 0.0866 T12: -0.0027 REMARK 3 T13: -0.0129 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 1.0948 L22: 0.2265 REMARK 3 L33: 1.1181 L12: -0.0636 REMARK 3 L13: -0.6714 L23: 0.0307 REMARK 3 S TENSOR REMARK 3 S11: 0.0165 S12: 0.0222 S13: -0.0917 REMARK 3 S21: -0.0399 S22: -0.0318 S23: 0.0195 REMARK 3 S31: 0.0338 S32: -0.0044 S33: 0.0187 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 220 THROUGH 265 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1700 43.4041 -3.8007 REMARK 3 T TENSOR REMARK 3 T11: 0.0918 T22: 0.0715 REMARK 3 T33: 0.0828 T12: 0.0111 REMARK 3 T13: 0.0095 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 2.5508 L22: 1.3736 REMARK 3 L33: 3.5300 L12: 0.1358 REMARK 3 L13: 0.3836 L23: -0.7399 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.0153 S13: -0.0128 REMARK 3 S21: -0.0460 S22: -0.0062 S23: -0.0836 REMARK 3 S31: -0.0027 S32: 0.1498 S33: 0.0203 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 4YAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207135. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-12 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 : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99996 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 115374 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.0000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 48.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 7.0, 1.5 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 80.48733 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 40.24367 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 40.24367 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 80.48733 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: 2820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 112.00133 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.24367 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 ALA A 2 REMARK 465 GLU A 3 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 HE ARG A 156 O HOH A 710 1.21 REMARK 500 H ASN A 64 O HOH A 403 1.43 REMARK 500 HH22 ARG A 81 O HOH A 402 1.49 REMARK 500 HE22 GLN A 5 OE2 GLU A 63 1.60 REMARK 500 O HOH A 789 O HOH A 827 1.81 REMARK 500 OD1 ASN A 64 O HOH A 401 1.87 REMARK 500 OE1 GLU A 126 O HOH A 779 1.91 REMARK 500 O HOH A 797 O HOH A 815 1.91 REMARK 500 OE1 GLU A 63 O HOH A 773 1.93 REMARK 500 O HOH A 525 O HOH A 526 1.96 REMARK 500 O HOH A 824 O HOH A 826 1.96 REMARK 500 O HOH A 801 O HOH A 839 1.97 REMARK 500 NE ARG A 156 O HOH A 710 1.97 REMARK 500 O HOH A 477 O HOH A 501 1.97 REMARK 500 O HOH A 812 O HOH A 837 1.98 REMARK 500 O HOH A 711 O HOH A 824 1.99 REMARK 500 O HOH A 556 O HOH A 785 2.00 REMARK 500 NH2 ARG A 81 O HOH A 402 2.01 REMARK 500 O HOH A 790 O HOH A 803 2.01 REMARK 500 O HOH A 472 O HOH A 534 2.06 REMARK 500 O HOH A 535 O HOH A 826 2.07 REMARK 500 O GLU A 6 O HOH A 762 2.07 REMARK 500 OE2 GLU A 36 O HOH A 705 2.07 REMARK 500 O HOH A 780 O HOH A 798 2.11 REMARK 500 N ASN A 64 O HOH A 403 2.12 REMARK 500 O HOH A 816 O HOH A 823 2.13 REMARK 500 O HOH A 734 O HOH A 837 2.14 REMARK 500 NE2 GLN A 5 OE2 GLU A 63 2.14 REMARK 500 NH1 ARG A 156 O HOH A 833 2.18 REMARK 500 OE1 GLU A 36 O HOH A 660 2.18 REMARK 500 O HOH A 497 O HOH A 515 2.19 REMARK 500 OD1 ASP A 179 O HOH A 725 2.19 REMARK 500 O GLU A 84 O HOH A 716 2.19 REMARK 500 OE2 GLU A 63 O HOH A 404 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 O HOH A 403 O HOH A 403 4465 1.24 REMARK 500 O HOH A 429 O HOH A 429 5675 1.64 REMARK 500 O HOH A 481 O HOH A 502 5675 1.71 REMARK 500 O HOH A 494 O HOH A 536 5675 1.83 REMARK 500 O HOH A 533 O HOH A 559 4465 1.98 REMARK 500 O HOH A 500 O HOH A 532 4565 2.12 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 LEU A 7 CA LEU A 7 C 0.192 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 ASP A 61 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 156 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = 3.8 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 70 102.73 82.81 REMARK 500 ASP A 150 -65.90 -126.41 REMARK 500 ASP A 154 -131.29 51.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LYS A 28 -13.29 REMARK 500 LYS A 28 12.51 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 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y98 RELATED DB: PDB REMARK 900 RELATED ID: 4Y9D RELATED DB: PDB REMARK 900 RELATED ID: 4YA6 RELATED DB: PDB REMARK 900 RELATED ID: 4YAC RELATED DB: PDB REMARK 900 RELATED ID: 4YAE RELATED DB: PDB REMARK 900 RELATED ID: 4YAG RELATED DB: PDB REMARK 900 RELATED ID: 4YAI RELATED DB: PDB REMARK 900 RELATED ID: 4YAM RELATED DB: PDB REMARK 900 RELATED ID: 4YAN RELATED DB: PDB REMARK 900 RELATED ID: 4YAV RELATED DB: PDB DBREF 4YAP A 1 265 UNP Q9WXJ9 Q9WXJ9_SPHPI 1 265 SEQRES 1 A 265 MET ALA GLU PRO GLN GLU LEU THR ILE TYR HIS ILE PRO SEQRES 2 A 265 GLY CYS PRO PHE SER GLU ARG VAL GLU ILE MET LEU GLU SEQRES 3 A 265 LEU LYS GLY LEU ARG MET LYS ASP VAL GLU ILE ASP ILE SEQRES 4 A 265 SER LYS PRO ARG PRO ASP TRP LEU LEU ALA LYS THR GLY SEQRES 5 A 265 GLY THR THR ALA LEU PRO LEU LEU ASP VAL GLU ASN GLY SEQRES 6 A 265 GLU SER LEU LYS GLU SER MET VAL ILE LEU ARG TYR LEU SEQRES 7 A 265 GLU GLN ARG TYR PRO GLU PRO ALA VAL ALA HIS PRO ASP SEQRES 8 A 265 PRO PHE CYS HIS ALA VAL GLU GLY MET LEU ALA GLU LEU SEQRES 9 A 265 ALA GLY PRO PHE SER GLY ALA GLY TYR ARG MET ILE LEU SEQRES 10 A 265 ASN ARG GLU ILE GLY LYS ARG GLU GLU MET ARG ALA ALA SEQRES 11 A 265 VAL ASP ALA GLU PHE GLY LYS VAL ASP ALA PHE LEU LYS SEQRES 12 A 265 ARG TYR ALA THR GLY SER ASP PHE LEU PHE ASP ASP ARG SEQRES 13 A 265 PHE GLY TRP ALA GLU VAL ALA PHE THR PRO MET PHE LYS SEQRES 14 A 265 ARG LEU TRP PHE LEU ASP TYR TYR GLU ASP TYR GLU VAL SEQRES 15 A 265 PRO ALA ASN PHE ASP ARG VAL LEU ARG TRP ARG ALA ALA SEQRES 16 A 265 CYS THR ALA HIS PRO ALA ALA GLN TYR ARG SER LYS GLU SEQRES 17 A 265 GLU LEU LEU LYS LEU TYR TYR ASP TYR THR GLN GLY GLY SEQRES 18 A 265 GLY ASN GLY ARG ILE PRO GLU GLY ARG SER ILE SER SER SEQRES 19 A 265 PHE SER PRO ASP VAL ASP TRP ARG THR ARG PRO MET PRO SEQRES 20 A 265 PRO ARG ASP LYS TRP GLY HIS ALA ALA THR ASP ALA GLU SEQRES 21 A 265 LEU GLY LEU THR ARG HET SO4 A 301 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *441(H2 O) HELIX 1 AA1 CYS A 15 LYS A 28 1 14 HELIX 2 AA2 PRO A 44 ALA A 49 1 6 HELIX 3 AA3 GLU A 63 GLY A 65 5 3 HELIX 4 AA4 GLU A 70 TYR A 82 1 13 HELIX 5 AA5 ASP A 91 LEU A 104 1 14 HELIX 6 AA6 LEU A 104 ASN A 118 1 15 HELIX 7 AA7 GLU A 120 GLY A 122 5 3 HELIX 8 AA8 LYS A 123 ALA A 146 1 24 HELIX 9 AA9 GLY A 158 LEU A 171 1 14 HELIX 10 AB1 LEU A 171 GLU A 178 1 8 HELIX 11 AB2 PHE A 186 HIS A 199 1 14 HELIX 12 AB3 PRO A 200 GLN A 203 5 4 HELIX 13 AB4 SER A 206 TYR A 214 1 9 HELIX 14 AB5 TYR A 215 GLY A 220 5 6 HELIX 15 AB6 ASP A 240 ARG A 244 5 5 SHEET 1 AA1 4 ARG A 31 GLU A 36 0 SHEET 2 AA1 4 GLU A 6 HIS A 11 1 N ILE A 9 O VAL A 35 SHEET 3 AA1 4 LEU A 59 ASP A 61 -1 O ASP A 61 N THR A 8 SHEET 4 AA1 4 SER A 67 LYS A 69 -1 O LEU A 68 N LEU A 60 CISPEP 1 LEU A 57 PRO A 58 0 2.78 CISPEP 2 GLU A 84 PRO A 85 0 -1.06 SITE 1 AC1 7 PRO A 42 ARG A 43 SER A 206 LYS A 207 SITE 2 AC1 7 GLU A 208 HOH A 409 HOH A 439 CRYST1 64.664 64.664 120.731 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 0.015465 0.008928 0.000000 0.00000 SCALE2 0.000000 0.017857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008283 0.00000