HEADER TRANSFERASE 02-MAY-09 3HAM TITLE STRUCTURE OF THE GENTAMICIN-APH(2")-IIA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOGLYCOSIDE PHOSPHOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS FAECIUM; SOURCE 4 ORGANISM_TAXID: 1352; SOURCE 5 GENE: APH(2')-IB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOGLYCOSIDE, GENTAMICIN, ANTIBIOTIC RESISTANCE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.G.YOUNG,E.N.BAKER,S.B.VAKULENKO,C.A.SMITH REVDAT 3 21-FEB-24 3HAM 1 COMPND REMARK HETNAM REVDAT 2 13-JUL-11 3HAM 1 VERSN REVDAT 1 28-JUL-09 3HAM 0 JRNL AUTH P.G.YOUNG,R.WALANJ,V.LAKSHMI,L.J.BYRNES,P.METCALF,E.N.BAKER, JRNL AUTH 2 S.B.VAKULENKO,C.A.SMITH JRNL TITL THE CRYSTAL STRUCTURES OF SUBSTRATE AND NUCLEOTIDE COMPLEXES JRNL TITL 2 OF ENTEROCOCCUS FAECIUM JRNL TITL 3 AMINOGLYCOSIDE-2''-PHOSPHOTRANSFERASE-IIA [APH(2'')-IIA] JRNL TITL 4 PROVIDE INSIGHTS INTO SUBSTRATE SELECTIVITY IN THE APH(2'') JRNL TITL 5 SUBFAMILY. JRNL REF J.BACTERIOL. V. 191 4133 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19429619 JRNL DOI 10.1128/JB.00149-09 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 24499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1299 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1688 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2990 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4978 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.55000 REMARK 3 B22 (A**2) : -3.12000 REMARK 3 B33 (A**2) : 0.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.681 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.322 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 25.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5158 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6944 ; 1.301 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 596 ; 5.694 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 276 ;36.529 ;25.072 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 968 ;19.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.919 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 764 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3834 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2565 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3532 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 327 ; 0.191 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.191 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.211 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3078 ; 0.602 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4824 ; 1.024 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2343 ; 1.656 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2120 ; 2.517 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 88 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0210 -5.0790 11.8800 REMARK 3 T TENSOR REMARK 3 T11: -0.1373 T22: 0.3329 REMARK 3 T33: -0.2910 T12: -0.0980 REMARK 3 T13: -0.0786 T23: -0.0010 REMARK 3 L TENSOR REMARK 3 L11: 4.8248 L22: 5.2567 REMARK 3 L33: 9.5704 L12: 1.7523 REMARK 3 L13: 2.2005 L23: 0.6224 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: -0.0458 S13: -0.2645 REMARK 3 S21: -0.9814 S22: -0.0293 S23: -0.0170 REMARK 3 S31: 0.7803 S32: -0.1178 S33: 0.0780 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 89 A 129 REMARK 3 RESIDUE RANGE : A 184 A 250 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7840 7.2590 28.8790 REMARK 3 T TENSOR REMARK 3 T11: -0.4706 T22: 0.4070 REMARK 3 T33: -0.4198 T12: 0.0008 REMARK 3 T13: -0.0359 T23: -0.0196 REMARK 3 L TENSOR REMARK 3 L11: 4.1053 L22: 3.2878 REMARK 3 L33: 3.9927 L12: -0.6779 REMARK 3 L13: -0.5659 L23: 0.6926 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: -0.7768 S13: 0.0996 REMARK 3 S21: -0.0196 S22: -0.0973 S23: -0.0332 REMARK 3 S31: -0.0057 S32: -0.4884 S33: 0.1115 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 130 A 183 REMARK 3 RESIDUE RANGE : A 251 A 299 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4210 -2.3950 20.1440 REMARK 3 T TENSOR REMARK 3 T11: -0.3372 T22: 0.2957 REMARK 3 T33: 0.0692 T12: 0.0693 REMARK 3 T13: 0.0052 T23: 0.1502 REMARK 3 L TENSOR REMARK 3 L11: 4.5722 L22: 2.6725 REMARK 3 L33: 5.8417 L12: 0.3117 REMARK 3 L13: -0.4327 L23: 1.7692 REMARK 3 S TENSOR REMARK 3 S11: 0.1845 S12: -0.1730 S13: -1.0611 REMARK 3 S21: -0.1397 S22: -0.2236 S23: -0.6910 REMARK 3 S31: 0.5151 S32: -0.0806 S33: 0.0391 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 88 REMARK 3 ORIGIN FOR THE GROUP (A): 50.9630 30.5670 10.7440 REMARK 3 T TENSOR REMARK 3 T11: -0.0160 T22: 0.4516 REMARK 3 T33: 0.1215 T12: -0.0944 REMARK 3 T13: 0.0384 T23: 0.0915 REMARK 3 L TENSOR REMARK 3 L11: 2.9387 L22: 3.9496 REMARK 3 L33: 8.0500 L12: 0.1129 REMARK 3 L13: -2.8628 L23: -0.1492 REMARK 3 S TENSOR REMARK 3 S11: 0.1312 S12: -0.0535 S13: 0.0664 REMARK 3 S21: -0.1524 S22: 0.0532 S23: -0.7870 REMARK 3 S31: -0.1013 S32: -0.0109 S33: -0.1844 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 89 B 129 REMARK 3 RESIDUE RANGE : B 184 B 250 REMARK 3 ORIGIN FOR THE GROUP (A): 40.3910 19.2250 28.2920 REMARK 3 T TENSOR REMARK 3 T11: -0.4724 T22: 0.5281 REMARK 3 T33: -0.2672 T12: -0.0836 REMARK 3 T13: -0.1601 T23: 0.1805 REMARK 3 L TENSOR REMARK 3 L11: 6.3112 L22: 5.7686 REMARK 3 L33: 3.4479 L12: -0.5259 REMARK 3 L13: -0.3063 L23: -0.4157 REMARK 3 S TENSOR REMARK 3 S11: 0.1700 S12: -0.9337 S13: -0.6052 REMARK 3 S21: 0.1017 S22: -0.1738 S23: -0.8414 REMARK 3 S31: -0.2913 S32: 0.6366 S33: 0.0038 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 130 B 183 REMARK 3 RESIDUE RANGE : B 251 B 299 REMARK 3 ORIGIN FOR THE GROUP (A): 20.1510 28.3700 18.9600 REMARK 3 T TENSOR REMARK 3 T11: -0.2544 T22: 0.3001 REMARK 3 T33: -0.3106 T12: 0.0676 REMARK 3 T13: -0.1074 T23: -0.0195 REMARK 3 L TENSOR REMARK 3 L11: 4.6244 L22: 3.8687 REMARK 3 L33: 6.8015 L12: -0.3753 REMARK 3 L13: 0.4476 L23: -0.2905 REMARK 3 S TENSOR REMARK 3 S11: 0.2279 S12: 0.0327 S13: 0.4413 REMARK 3 S21: -0.4324 S22: -0.3612 S23: 0.2367 REMARK 3 S31: -0.7731 S32: 0.1667 S33: 0.1333 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3HAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052900. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-04 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL, LN REMARK 200 COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 80.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: UNBUFFERED 16% PEG 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 29.40000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY B 239 O VAL B 242 1.96 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 LEU A 24 -65.67 -109.31 REMARK 500 SER A 26 81.72 -165.43 REMARK 500 ASN A 36 14.65 52.62 REMARK 500 GLN A 38 -30.18 -142.45 REMARK 500 LYS A 67 81.72 68.75 REMARK 500 ARG A 92 -168.40 64.82 REMARK 500 ILE A 93 87.47 55.28 REMARK 500 CYS A 127 24.12 -63.14 REMARK 500 ASN A 191 -2.80 75.52 REMARK 500 ASP A 192 53.70 -148.93 REMARK 500 ASP A 210 72.37 55.44 REMARK 500 ASP A 233 -128.27 -117.86 REMARK 500 SER B 26 -92.15 -96.57 REMARK 500 ASN B 36 19.84 53.76 REMARK 500 GLN B 38 -4.78 -163.04 REMARK 500 ARG B 46 148.43 177.88 REMARK 500 ASN B 65 42.49 -99.35 REMARK 500 SER B 102 127.14 90.02 REMARK 500 CYS B 127 -12.06 60.14 REMARK 500 ASN B 191 -0.51 76.15 REMARK 500 ASP B 192 40.77 -146.94 REMARK 500 ASP B 210 70.32 45.55 REMARK 500 ASP B 233 -132.85 -119.49 REMARK 500 LEU B 243 -63.57 122.13 REMARK 500 TYR B 246 -20.65 112.58 REMARK 500 ALA B 250 73.07 -150.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 91 ARG A 92 137.22 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 LLL A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LLL B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HAV RELATED DB: PDB DBREF 3HAM A 1 299 UNP Q9EVD7 Q9EVD7_ENTFC 1 299 DBREF 3HAM B 1 299 UNP Q9EVD7 Q9EVD7_ENTFC 1 299 SEQRES 1 A 299 MET VAL ASN LEU ASP ALA GLU ILE TYR GLU HIS LEU ASN SEQRES 2 A 299 LYS GLN ILE LYS ILE ASN GLU LEU ARG TYR LEU SER SER SEQRES 3 A 299 GLY ASP ASP SER ASP THR PHE LEU CYS ASN GLU GLN TYR SEQRES 4 A 299 VAL VAL LYS VAL PRO LYS ARG ASP SER VAL ARG ILE SER SEQRES 5 A 299 GLN LYS ARG GLU PHE GLU LEU TYR ARG PHE LEU GLU ASN SEQRES 6 A 299 CYS LYS LEU SER TYR GLN ILE PRO ALA VAL VAL TYR GLN SEQRES 7 A 299 SER ASP ARG PHE ASN ILE MET LYS TYR ILE LYS GLY GLU SEQRES 8 A 299 ARG ILE THR TYR GLU GLN TYR HIS LYS LEU SER GLU LYS SEQRES 9 A 299 GLU LYS ASP ALA LEU ALA TYR ASP GLU ALA THR PHE LEU SEQRES 10 A 299 LYS GLU LEU HIS SER ILE GLU ILE ASP CYS SER VAL SER SEQRES 11 A 299 LEU PHE SER ASP ALA LEU VAL ASN LYS LYS ASP LYS PHE SEQRES 12 A 299 LEU GLN ASP LYS LYS LEU LEU ILE SER ILE LEU GLU LYS SEQRES 13 A 299 GLU GLN LEU LEU THR ASP GLU MET LEU GLU HIS ILE GLU SEQRES 14 A 299 THR ILE TYR GLU ASN ILE LEU ASN ASN ALA VAL LEU PHE SEQRES 15 A 299 LYS TYR THR PRO CYS LEU VAL HIS ASN ASP PHE SER ALA SEQRES 16 A 299 ASN ASN MET ILE PHE ARG ASN ASN ARG LEU PHE GLY VAL SEQRES 17 A 299 ILE ASP PHE GLY ASP PHE ASN VAL GLY ASP PRO ASP ASN SEQRES 18 A 299 ASP PHE LEU CYS LEU LEU ASP CYS SER THR ASP ASP PHE SEQRES 19 A 299 GLY LYS GLU PHE GLY ARG LYS VAL LEU LYS TYR TYR GLN SEQRES 20 A 299 HIS LYS ALA PRO GLU VAL ALA GLU ARG LYS ALA GLU LEU SEQRES 21 A 299 ASN ASP VAL TYR TRP SER ILE ASP GLN ILE ILE TYR GLY SEQRES 22 A 299 TYR GLU ARG LYS ASP ARG GLU MET LEU ILE LYS GLY VAL SEQRES 23 A 299 SER GLU LEU LEU GLN THR GLN ALA GLU MET PHE ILE PHE SEQRES 1 B 299 MET VAL ASN LEU ASP ALA GLU ILE TYR GLU HIS LEU ASN SEQRES 2 B 299 LYS GLN ILE LYS ILE ASN GLU LEU ARG TYR LEU SER SER SEQRES 3 B 299 GLY ASP ASP SER ASP THR PHE LEU CYS ASN GLU GLN TYR SEQRES 4 B 299 VAL VAL LYS VAL PRO LYS ARG ASP SER VAL ARG ILE SER SEQRES 5 B 299 GLN LYS ARG GLU PHE GLU LEU TYR ARG PHE LEU GLU ASN SEQRES 6 B 299 CYS LYS LEU SER TYR GLN ILE PRO ALA VAL VAL TYR GLN SEQRES 7 B 299 SER ASP ARG PHE ASN ILE MET LYS TYR ILE LYS GLY GLU SEQRES 8 B 299 ARG ILE THR TYR GLU GLN TYR HIS LYS LEU SER GLU LYS SEQRES 9 B 299 GLU LYS ASP ALA LEU ALA TYR ASP GLU ALA THR PHE LEU SEQRES 10 B 299 LYS GLU LEU HIS SER ILE GLU ILE ASP CYS SER VAL SER SEQRES 11 B 299 LEU PHE SER ASP ALA LEU VAL ASN LYS LYS ASP LYS PHE SEQRES 12 B 299 LEU GLN ASP LYS LYS LEU LEU ILE SER ILE LEU GLU LYS SEQRES 13 B 299 GLU GLN LEU LEU THR ASP GLU MET LEU GLU HIS ILE GLU SEQRES 14 B 299 THR ILE TYR GLU ASN ILE LEU ASN ASN ALA VAL LEU PHE SEQRES 15 B 299 LYS TYR THR PRO CYS LEU VAL HIS ASN ASP PHE SER ALA SEQRES 16 B 299 ASN ASN MET ILE PHE ARG ASN ASN ARG LEU PHE GLY VAL SEQRES 17 B 299 ILE ASP PHE GLY ASP PHE ASN VAL GLY ASP PRO ASP ASN SEQRES 18 B 299 ASP PHE LEU CYS LEU LEU ASP CYS SER THR ASP ASP PHE SEQRES 19 B 299 GLY LYS GLU PHE GLY ARG LYS VAL LEU LYS TYR TYR GLN SEQRES 20 B 299 HIS LYS ALA PRO GLU VAL ALA GLU ARG LYS ALA GLU LEU SEQRES 21 B 299 ASN ASP VAL TYR TRP SER ILE ASP GLN ILE ILE TYR GLY SEQRES 22 B 299 TYR GLU ARG LYS ASP ARG GLU MET LEU ILE LYS GLY VAL SEQRES 23 B 299 SER GLU LEU LEU GLN THR GLN ALA GLU MET PHE ILE PHE HET LLL A 500 31 HET GOL A 300 6 HET GOL A 301 6 HET LLL B 500 31 HET GOL B 300 6 HET GOL B 301 6 HETNAM LLL (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R, HETNAM 2 LLL 3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2- HETNAM 3 LLL YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4- HETNAM 4 LLL (METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL HETNAM GOL GLYCEROL HETSYN LLL GENTAMICIN C1A HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 LLL 2(C19 H39 N5 O7) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 9 HOH *238(H2 O) HELIX 1 1 ASP A 5 ILE A 16 1 12 HELIX 2 2 ASP A 47 GLU A 64 1 18 HELIX 3 3 THR A 94 HIS A 99 1 6 HELIX 4 4 SER A 102 ILE A 123 1 22 HELIX 5 5 VAL A 129 ASP A 134 1 6 HELIX 6 6 ASN A 138 GLU A 157 1 20 HELIX 7 7 THR A 161 ASN A 177 1 17 HELIX 8 8 ASN A 178 LYS A 183 5 6 HELIX 9 9 SER A 194 ASN A 196 5 3 HELIX 10 10 ASP A 218 PHE A 223 5 6 HELIX 11 11 GLY A 235 TYR A 245 1 11 HELIX 12 12 ALA A 250 TYR A 264 1 15 HELIX 13 13 TYR A 264 ARG A 276 1 13 HELIX 14 14 ASP A 278 LEU A 290 1 13 HELIX 15 15 GLN A 291 THR A 292 5 2 HELIX 16 16 GLN A 293 ILE A 298 5 6 HELIX 17 17 ASP B 5 ILE B 16 1 12 HELIX 18 18 ARG B 46 GLU B 64 1 19 HELIX 19 19 THR B 94 HIS B 99 1 6 HELIX 20 20 SER B 102 HIS B 121 1 20 HELIX 21 21 VAL B 129 ASP B 134 1 6 HELIX 22 22 ASN B 138 GLU B 157 1 20 HELIX 23 23 THR B 161 ASN B 177 1 17 HELIX 24 24 ASN B 178 LYS B 183 5 6 HELIX 25 25 SER B 194 ASN B 196 5 3 HELIX 26 26 ASP B 218 LEU B 224 5 7 HELIX 27 27 GLY B 235 LYS B 244 1 10 HELIX 28 28 ALA B 250 TYR B 264 1 15 HELIX 29 29 TYR B 264 ARG B 276 1 13 HELIX 30 30 ASP B 278 LEU B 290 1 13 HELIX 31 31 GLN B 291 THR B 292 5 2 HELIX 32 32 GLN B 293 ILE B 298 5 6 SHEET 1 A 5 LEU A 21 SER A 26 0 SHEET 2 A 5 SER A 30 CYS A 35 -1 O LEU A 34 N ARG A 22 SHEET 3 A 5 TYR A 39 PRO A 44 -1 O VAL A 41 N PHE A 33 SHEET 4 A 5 ASN A 83 LYS A 86 -1 O ASN A 83 N LYS A 42 SHEET 5 A 5 VAL A 75 TYR A 77 -1 N VAL A 76 O ILE A 84 SHEET 1 B 2 CYS A 187 VAL A 189 0 SHEET 2 B 2 ASN A 215 GLY A 217 -1 O ASN A 215 N VAL A 189 SHEET 1 C 2 MET A 198 ARG A 201 0 SHEET 2 C 2 ARG A 204 VAL A 208 -1 O ARG A 204 N ARG A 201 SHEET 1 D 5 LEU B 21 SER B 25 0 SHEET 2 D 5 SER B 30 CYS B 35 -1 O THR B 32 N SER B 25 SHEET 3 D 5 TYR B 39 PRO B 44 -1 O TYR B 39 N CYS B 35 SHEET 4 D 5 ASN B 83 LYS B 86 -1 O ASN B 83 N LYS B 42 SHEET 5 D 5 VAL B 75 GLN B 78 -1 N TYR B 77 O ILE B 84 SHEET 1 E 2 CYS B 187 VAL B 189 0 SHEET 2 E 2 ASN B 215 GLY B 217 -1 O ASN B 215 N VAL B 189 SHEET 1 F 2 MET B 198 ARG B 201 0 SHEET 2 F 2 ARG B 204 VAL B 208 -1 O GLY B 207 N ILE B 199 SITE 1 AC1 15 ASP A 192 SER A 194 ASN A 196 ASP A 213 SITE 2 AC1 15 ASP A 228 SER A 230 ASP A 232 ASP A 262 SITE 3 AC1 15 TRP A 265 ARG A 276 HOH A 307 HOH A 308 SITE 4 AC1 15 HOH A 380 HOH A 389 HOH A 397 SITE 1 AC2 5 PHE A 182 LYS A 183 TYR A 184 PRO A 186 SITE 2 AC2 5 HOH A 340 SITE 1 AC3 6 ASN A 191 ASN A 221 CYS A 225 ASN A 261 SITE 2 AC3 6 HOH A 303 HOH A 341 SITE 1 AC4 13 ASP B 192 SER B 194 ASN B 196 ASP B 213 SITE 2 AC4 13 ASP B 228 SER B 230 ASP B 232 ASP B 262 SITE 3 AC4 13 HOH B 304 HOH B 345 HOH B 352 HOH B 391 SITE 4 AC4 13 HOH B 407 SITE 1 AC5 1 HOH B 363 SITE 1 AC6 2 TYR B 245 HOH B 390 CRYST1 79.700 58.800 81.400 90.00 98.40 90.00 P 1 21 1 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 0.012547 0.000000 0.001853 0.00000 SCALE2 0.000000 0.017007 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012418 0.00000