HEADER BIOSYNTHETIC PROTEIN 15-AUG-15 5D86 TITLE STAPHYLOFERRIN B PRECURSOR BIOSYNTHETIC ENZYME SBNA Y152F VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE SIDEROPHORE BIOSYNTHESIS PROTEIN SBNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 426430; SOURCE 4 STRAIN: NEWMAN; SOURCE 5 GENE: SBNA, NWMN_0060; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS SIDEROPHORE, IRON, PLP, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.KOBYLARZ,J.C.GRIGG,Y.LIU,M.S.F.LEE,D.E.HEINRICHS,M.E.P.MURPHY REVDAT 3 08-JAN-20 5D86 1 JRNL REMARK REVDAT 2 24-FEB-16 5D86 1 JRNL REVDAT 1 03-FEB-16 5D86 0 JRNL AUTH M.J.KOBYLARZ,J.C.GRIGG,Y.LIU,M.S.LEE,D.E.HEINRICHS, JRNL AUTH 2 M.E.MURPHY JRNL TITL DECIPHERING THE SUBSTRATE SPECIFICITY OF SBNA, THE ENZYME JRNL TITL 2 CATALYZING THE FIRST STEP IN STAPHYLOFERRIN B BIOSYNTHESIS. JRNL REF BIOCHEMISTRY V. 55 927 2016 JRNL REFN ISSN 0006-2960 JRNL PMID 26794841 JRNL DOI 10.1021/ACS.BIOCHEM.5B01045 REMARK 2 REMARK 2 RESOLUTION. 1.50 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.38 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 47644 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2412 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 35.3892 - 3.8554 0.99 2900 153 0.1376 0.1574 REMARK 3 2 3.8554 - 3.0607 0.99 2762 155 0.1359 0.1560 REMARK 3 3 3.0607 - 2.6739 1.00 2693 173 0.1524 0.1813 REMARK 3 4 2.6739 - 2.4295 1.00 2757 131 0.1530 0.1909 REMARK 3 5 2.4295 - 2.2554 1.00 2718 146 0.1485 0.1967 REMARK 3 6 2.2554 - 2.1225 1.00 2731 140 0.1446 0.1845 REMARK 3 7 2.1225 - 2.0162 1.00 2685 130 0.1467 0.1690 REMARK 3 8 2.0162 - 1.9284 1.00 2723 137 0.1512 0.1875 REMARK 3 9 1.9284 - 1.8542 1.00 2705 133 0.1577 0.1957 REMARK 3 10 1.8542 - 1.7902 1.00 2687 151 0.1565 0.2205 REMARK 3 11 1.7902 - 1.7342 1.00 2642 153 0.1571 0.1963 REMARK 3 12 1.7342 - 1.6847 1.00 2666 145 0.1515 0.1910 REMARK 3 13 1.6847 - 1.6403 1.00 2684 150 0.1504 0.1899 REMARK 3 14 1.6403 - 1.6003 1.00 2700 126 0.1583 0.1877 REMARK 3 15 1.6003 - 1.5639 0.95 2519 151 0.1614 0.1996 REMARK 3 16 1.5639 - 1.5306 0.90 2408 124 0.1706 0.1972 REMARK 3 17 1.5306 - 1.5000 0.84 2252 114 0.1830 0.2037 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.920 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.13 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 : 0.014 2726 REMARK 3 ANGLE : 1.527 3722 REMARK 3 CHIRALITY : 0.067 420 REMARK 3 PLANARITY : 0.010 483 REMARK 3 DIHEDRAL : 14.214 1041 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 8:118 ) REMARK 3 ORIGIN FOR THE GROUP (A): 19.6962 -8.1691 -4.4832 REMARK 3 T TENSOR REMARK 3 T11: 0.0914 T22: 0.0702 REMARK 3 T33: 0.0821 T12: -0.0070 REMARK 3 T13: -0.0187 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 1.9774 L22: 0.7339 REMARK 3 L33: 0.5276 L12: -0.2236 REMARK 3 L13: -0.3880 L23: -0.0949 REMARK 3 S TENSOR REMARK 3 S11: 0.0905 S12: 0.0612 S13: -0.0315 REMARK 3 S21: -0.0110 S22: -0.0372 S23: 0.0903 REMARK 3 S31: -0.0385 S32: -0.0346 S33: -0.0534 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 119:142 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.6806 -20.6195 13.1999 REMARK 3 T TENSOR REMARK 3 T11: 0.2538 T22: 0.1772 REMARK 3 T33: 0.2187 T12: -0.0146 REMARK 3 T13: -0.0492 T23: 0.0359 REMARK 3 L TENSOR REMARK 3 L11: 4.7600 L22: 4.3703 REMARK 3 L33: 2.8344 L12: -0.0451 REMARK 3 L13: 0.3931 L23: 0.1421 REMARK 3 S TENSOR REMARK 3 S11: -0.0193 S12: -0.6562 S13: -0.4383 REMARK 3 S21: 0.7331 S22: 0.0684 S23: -0.4407 REMARK 3 S31: 0.1128 S32: 0.1316 S33: 0.1415 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 143:231 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.9012 -21.2865 -7.9660 REMARK 3 T TENSOR REMARK 3 T11: 0.0958 T22: 0.0579 REMARK 3 T33: 0.0947 T12: -0.0003 REMARK 3 T13: -0.0147 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 1.7346 L22: 0.7220 REMARK 3 L33: 0.8531 L12: -0.2207 REMARK 3 L13: -0.5945 L23: -0.0075 REMARK 3 S TENSOR REMARK 3 S11: 0.0060 S12: 0.1048 S13: -0.1940 REMARK 3 S21: -0.0730 S22: -0.0290 S23: 0.0834 REMARK 3 S31: 0.0607 S32: -0.0285 S33: 0.0247 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN A AND RESID 232:325 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.7954 -17.4718 0.6484 REMARK 3 T TENSOR REMARK 3 T11: 0.0654 T22: 0.0718 REMARK 3 T33: 0.0598 T12: 0.0130 REMARK 3 T13: 0.0061 T23: 0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.8325 L22: 1.5959 REMARK 3 L33: 1.0478 L12: -0.0278 REMARK 3 L13: 0.0255 L23: 0.0747 REMARK 3 S TENSOR REMARK 3 S11: 0.0165 S12: -0.0599 S13: -0.0735 REMARK 3 S21: 0.1482 S22: -0.0071 S23: -0.0231 REMARK 3 S31: 0.0536 S32: 0.0765 S33: -0.0051 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 5D86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212815. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12709 REMARK 200 MONOCHROMATOR : SIDE SCATTERING I-BEAM BENT REMARK 200 SINGLE CRYSTAL; ASYMMETRIC CUT REMARK 200 4.9650 DEG. REMARK 200 OPTICS : RH COATED FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.15 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 57.995 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 18.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.20800 REMARK 200 R SYM FOR SHELL (I) : 0.20800 REMARK 200 FOR SHELL : 3.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.5 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M TRIS, PH 8.5, 29 REMARK 280 -33% PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 28.18000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.18000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.99500 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: 5110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 56.36000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 A1279 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1405 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 MET A 1 REMARK 465 ILE A 2 REMARK 465 GLU A 3 REMARK 465 LYS A 4 REMARK 465 SER A 5 REMARK 465 GLN A 6 REMARK 465 ALA A 7 REMARK 465 GLU A 326 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 O HOH A 1339 O HOH A 1375 2.02 REMARK 500 O1 TRS A 1004 O HOH A 1101 2.04 REMARK 500 O HOH A 1363 O HOH A 1445 2.16 REMARK 500 OD2 ASP A 263 O HOH A 1102 2.16 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 1118 O HOH A 1380 2655 1.99 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 ASP A 145 75.38 59.85 REMARK 500 SER A 185 -68.29 -139.26 REMARK 500 LEU A 307 -112.50 -110.65 REMARK 500 LEU A 307 -110.96 -113.16 REMARK 500 GLN A 321 31.25 -71.82 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 HIS A 25 0.07 SIDE CHAIN 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 A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1429 O REMARK 620 2 HOH A1166 O 88.8 REMARK 620 3 HOH A1210 O 88.9 91.6 REMARK 620 4 HOH A1167 O 86.7 93.4 173.3 REMARK 620 5 HOH A1385 O 172.4 84.2 88.2 96.7 REMARK 620 6 HOH A1432 O 92.8 178.0 89.5 85.6 94.2 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 PLP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5D84 RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH PLP REMARK 900 RELATED ID: 5D85 RELATED DB: PDB REMARK 900 RELATED ID: 5D87 RELATED DB: PDB DBREF 5D86 A 1 326 UNP A6QDA0 SBNA_STAAE 1 326 SEQADV 5D86 PHE A 152 UNP A6QDA0 TYR 152 ENGINEERED MUTATION SEQRES 1 A 326 MET ILE GLU LYS SER GLN ALA CYS HIS ASP SER LEU LEU SEQRES 2 A 326 ASP SER VAL GLY GLN THR PRO MET VAL GLN LEU HIS GLN SEQRES 3 A 326 LEU PHE PRO LYS HIS GLU VAL PHE ALA LYS LEU GLU TYR SEQRES 4 A 326 MET ASN PRO GLY GLY SER MET LYS ASP ARG PRO ALA LYS SEQRES 5 A 326 TYR ILE ILE GLU HIS GLY ILE LYS HIS GLY LEU ILE THR SEQRES 6 A 326 GLU ASN THR HIS LEU ILE GLU SER THR SER GLY ASN LEU SEQRES 7 A 326 GLY ILE ALA LEU ALA MET ILE ALA LYS ILE LYS GLY LEU SEQRES 8 A 326 LYS LEU THR CYS VAL VAL ASP PRO LYS ILE SER PRO THR SEQRES 9 A 326 ASN LEU LYS ILE ILE LYS SER TYR GLY ALA ASN VAL GLU SEQRES 10 A 326 MET VAL GLU GLU PRO ASP ALA HIS GLY GLY TYR LEU MET SEQRES 11 A 326 THR ARG ILE ALA LYS VAL GLN GLU LEU LEU ALA THR ILE SEQRES 12 A 326 ASP ASP ALA TYR TRP ILE ASN GLN PHE ALA ASN GLU LEU SEQRES 13 A 326 ASN TRP GLN SER HIS TYR HIS GLY ALA GLY THR GLU ILE SEQRES 14 A 326 VAL GLU THR ILE LYS GLN PRO ILE ASP TYR PHE VAL ALA SEQRES 15 A 326 PRO VAL SER THR THR GLY SER ILE MET GLY MET SER ARG SEQRES 16 A 326 LYS ILE LYS GLU VAL HIS PRO ASN ALA GLN ILE VAL ALA SEQRES 17 A 326 VAL ASP ALA LYS GLY SER VAL ILE PHE GLY ASP LYS PRO SEQRES 18 A 326 ILE ASN ARG GLU LEU PRO GLY ILE GLY ALA SER ARG VAL SEQRES 19 A 326 PRO GLU ILE LEU ASN ARG SER GLU ILE ASN GLN VAL ILE SEQRES 20 A 326 HIS VAL ASP ASP TYR GLN SER ALA LEU GLY CYS ARG LYS SEQRES 21 A 326 LEU ILE ASP TYR GLU GLY ILE PHE ALA GLY GLY SER THR SEQRES 22 A 326 GLY SER ILE ILE ALA ALA ILE GLU GLN LEU ILE THR SER SEQRES 23 A 326 ILE GLU GLU GLY ALA THR ILE VAL THR ILE LEU PRO ASP SEQRES 24 A 326 ARG GLY ASP ARG TYR LEU ASP LEU VAL TYR SER ASP THR SEQRES 25 A 326 TRP LEU GLU LYS MET LYS SER ARG GLN GLY VAL LYS SER SEQRES 26 A 326 GLU HET PLP A1001 15 HET MG A1002 1 HET MG A1003 1 HET TRS A1004 8 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN TRS TRIS BUFFER FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 MG 2(MG 2+) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *351(H2 O) HELIX 1 AA1 SER A 11 VAL A 16 5 6 HELIX 2 AA2 GLU A 38 ASN A 41 5 4 HELIX 3 AA3 LYS A 47 HIS A 61 1 15 HELIX 4 AA4 GLY A 76 GLY A 90 1 15 HELIX 5 AA5 SER A 102 TYR A 112 1 11 HELIX 6 AA6 TYR A 128 ILE A 143 1 16 HELIX 7 AA7 ASN A 154 GLY A 164 1 11 HELIX 8 AA8 GLY A 164 ILE A 173 1 10 HELIX 9 AA9 THR A 187 HIS A 201 1 15 HELIX 10 AB1 ASN A 239 ILE A 243 5 5 HELIX 11 AB2 ASP A 250 GLY A 266 1 17 HELIX 12 AB3 GLY A 270 THR A 285 1 16 HELIX 13 AB4 ARG A 300 LEU A 305 5 6 HELIX 14 AB5 SER A 310 SER A 319 1 10 HELIX 15 AB6 ARG A 320 SER A 325 5 6 SHEET 1 AA1 6 MET A 21 GLN A 23 0 SHEET 2 AA1 6 GLU A 32 LYS A 36 -1 O ALA A 35 N VAL A 22 SHEET 3 AA1 6 THR A 292 ILE A 296 1 O ILE A 293 N PHE A 34 SHEET 4 AA1 6 TYR A 179 PRO A 183 1 N VAL A 181 O VAL A 294 SHEET 5 AA1 6 GLN A 205 ALA A 211 1 O VAL A 207 N PHE A 180 SHEET 6 AA1 6 GLN A 245 VAL A 249 1 O GLN A 245 N ALA A 208 SHEET 1 AA2 4 ASN A 115 MET A 118 0 SHEET 2 AA2 4 LEU A 93 VAL A 97 1 N LEU A 93 O ASN A 115 SHEET 3 AA2 4 HIS A 69 SER A 73 1 N LEU A 70 O THR A 94 SHEET 4 AA2 4 ALA A 146 TRP A 148 1 O TYR A 147 N ILE A 71 LINK NZ LYS A 47 C4A PLP A1001 1555 1555 1.31 LINK MG MG A1002 O HOH A1429 1555 1555 2.18 LINK MG MG A1002 O HOH A1166 1555 1555 2.04 LINK MG MG A1002 O HOH A1210 1555 1555 2.18 LINK MG MG A1003 O HOH A1136 1555 1555 2.95 LINK MG MG A1002 O HOH A1167 1555 1455 2.24 LINK MG MG A1002 O HOH A1385 1555 1455 2.18 LINK MG MG A1002 O HOH A1432 1555 1455 2.20 SITE 1 AC1 15 LYS A 47 ASN A 77 VAL A 184 SER A 185 SITE 2 AC1 15 THR A 186 THR A 187 GLY A 188 SER A 189 SITE 3 AC1 15 GLY A 228 SER A 272 PRO A 298 ASP A 299 SITE 4 AC1 15 HOH A1170 HOH A1207 HOH A1260 SITE 1 AC2 6 HOH A1166 HOH A1167 HOH A1210 HOH A1385 SITE 2 AC2 6 HOH A1429 HOH A1432 SITE 1 AC3 3 SER A 232 ARG A 233 HOH A1136 SITE 1 AC4 10 GLN A 26 ASN A 67 LYS A 87 ILE A 88 SITE 2 AC4 10 GLY A 90 ASP A 263 TYR A 264 HOH A1101 SITE 3 AC4 10 HOH A1118 HOH A1277 CRYST1 56.360 115.990 45.450 90.00 90.00 90.00 P 21 21 2 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 0.017743 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022002 0.00000