HEADER TRANSPORT PROTEIN 19-JAN-11 2Y5Y TITLE CRYSTAL STRUCTURE OF LACY IN COMPLEX WITH AN AFFINITY INACTIVATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTOSE PERMEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LACTOSE-PROTON SYMPORT; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: METHANE-THIO-SULFONIDE-GALACTOSIDE LINKED BY S-S BOND COMPND 8 TO C122. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 ATCC: 27325; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET18 KEYWDS TRANSPORT PROTEIN, AFFINITY INACTIVATION EXPDTA X-RAY DIFFRACTION AUTHOR V.CHAPTAL,S.KWON,M.R.SAWAYA,L.GUAN,H.R.KABACK,J.ABRAMSON REVDAT 4 20-DEC-23 2Y5Y 1 COMPND HETNAM HETSYN REVDAT 3 29-JUL-20 2Y5Y 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 06-JUL-11 2Y5Y 1 JRNL REVDAT 1 15-JUN-11 2Y5Y 0 JRNL AUTH V.CHAPTAL,S.KWON,M.R.SAWAYA,L.GUAN,H.R.KABACK,J.ABRAMSON JRNL TITL CRYSTAL STRUCTURE OF LACTOSE PERMEASE IN COMPLEX WITH AN JRNL TITL 2 AFFINITY INACTIVATOR YIELDS UNIQUE INSIGHT INTO SUGAR JRNL TITL 3 RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 9361 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21593407 JRNL DOI 10.1073/PNAS.1105687108 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.GUAN,M.SAHIN-TOTH,T.KALAI,K.HIDEG,H.R.KABACK REMARK 1 TITL PROBING THE MECHANISM OF A MEMBRANE TRANSPORT PROTEIN WITH REMARK 1 TITL 2 AFFINITY INACTIVATORS. REMARK 1 REF J.BIOL.CHEM. V. 278 10641 2003 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 12471022 REMARK 1 DOI 10.1074/JBC.M211355200 REMARK 2 REMARK 2 RESOLUTION. 3.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.8.0 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 35055 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) : 0.287 REMARK 3 R VALUE (WORKING SET) : 0.286 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.38 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.48 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2540 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2823 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2413 REMARK 3 BIN R VALUE (WORKING SET) : 0.2822 REMARK 3 BIN FREE R VALUE : 0.2843 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 127 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6177 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 163.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -9.83980 REMARK 3 B22 (A**2) : -6.58990 REMARK 3 B33 (A**2) : 16.42970 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 1.298 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.875 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.857 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6399 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 8661 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2147 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 79 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 952 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6369 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 813 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 7546 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.00 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.04 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 22.15 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN B AND (RESID 4:801) REMARK 3 ORIGIN FOR THE GROUP (A): 31.1006 111.1620 165.2110 REMARK 3 T TENSOR REMARK 3 T11: 0.3659 T22: 0.3224 REMARK 3 T33: -0.2413 T12: -0.1511 REMARK 3 T13: -0.0164 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 2.1245 L22: 4.3839 REMARK 3 L33: 8.3308 L12: -1.5090 REMARK 3 L13: 0.4056 L23: -0.4278 REMARK 3 S TENSOR REMARK 3 S11: 0.0804 S12: -0.0379 S13: -0.0069 REMARK 3 S21: 0.3248 S22: -0.0957 S23: -0.0957 REMARK 3 S31: 0.3882 S32: 0.3107 S33: 0.0153 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 4:701) REMARK 3 ORIGIN FOR THE GROUP (A): 59.3230 69.1850 167.6080 REMARK 3 T TENSOR REMARK 3 T11: 0.3664 T22: 0.1761 REMARK 3 T33: -0.2420 T12: -0.1270 REMARK 3 T13: 0.0720 T23: -0.0469 REMARK 3 L TENSOR REMARK 3 L11: 0.0000 L22: 3.4507 REMARK 3 L33: 8.3216 L12: -1.3823 REMARK 3 L13: 0.3737 L23: -0.7672 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: 0.2643 S13: -0.0837 REMARK 3 S21: 0.2322 S22: -0.0718 S23: 0.2314 REMARK 3 S31: -0.1328 S32: -0.5405 S33: 0.0711 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Y5Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1290047044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35055 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 REMARK 200 RESOLUTION RANGE LOW (A) : 28.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.74000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: PDB ENTRY 1PV7 REMARK 200 REMARK 200 REMARK: THE DATA DISPLAYED STRONG ANISOTROPY. THE NON- CORRECTED REMARK 200 DATA WAS DEPOSITED IN THE PDB, WHILE THE CORRECTED DATA WAS REMARK 200 INITIALLY USED TO SOLVE THE STRUCTURE, WITH BETTER DATA REMARK 200 STATISTICS IN THE HIGH RESOLUTION SHELLS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 82.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 7.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6 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 51.28000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 94.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 94.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.28000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.92000 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: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.2 KCAL/MOL 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 117 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, ALA 122 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 148 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 154 TO VAL REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 176 TO MET REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 234 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 333 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 353 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, CYS 355 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 117 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, ALA 122 TO CYS REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 148 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 154 TO VAL REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 176 TO MET REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 234 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 333 TO SER REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 353 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, CYS 355 TO ALA 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 TYR A 2 REMARK 465 TYR A 3 REMARK 465 THR A 189 REMARK 465 ASP A 190 REMARK 465 ALA A 191 REMARK 465 PRO A 192 REMARK 465 SER A 193 REMARK 465 SER A 194 REMARK 465 ALA A 195 REMARK 465 THR A 196 REMARK 465 VAL A 197 REMARK 465 ALA A 198 REMARK 465 ASN A 199 REMARK 465 ALA A 200 REMARK 465 VAL A 201 REMARK 465 GLY A 202 REMARK 465 GLY A 404 REMARK 465 PRO A 405 REMARK 465 LEU A 406 REMARK 465 SER A 407 REMARK 465 LEU A 408 REMARK 465 LEU A 409 REMARK 465 ARG A 410 REMARK 465 ARG A 411 REMARK 465 GLN A 412 REMARK 465 VAL A 413 REMARK 465 ASN A 414 REMARK 465 GLU A 415 REMARK 465 VAL A 416 REMARK 465 ALA A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 HIS A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 MET B 1 REMARK 465 TYR B 2 REMARK 465 TYR B 3 REMARK 465 ASP B 190 REMARK 465 ALA B 191 REMARK 465 PRO B 192 REMARK 465 SER B 193 REMARK 465 SER B 194 REMARK 465 ALA B 195 REMARK 465 THR B 196 REMARK 465 PRO B 405 REMARK 465 LEU B 406 REMARK 465 SER B 407 REMARK 465 LEU B 408 REMARK 465 LEU B 409 REMARK 465 ARG B 410 REMARK 465 ARG B 411 REMARK 465 GLN B 412 REMARK 465 VAL B 413 REMARK 465 ASN B 414 REMARK 465 GLU B 415 REMARK 465 VAL B 416 REMARK 465 ALA B 417 REMARK 465 HIS B 418 REMARK 465 HIS B 419 REMARK 465 HIS B 420 REMARK 465 HIS B 421 REMARK 465 HIS B 422 REMARK 465 HIS B 423 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 A 231 OG1 THR A 235 2.06 REMARK 500 O GLY B 231 OG1 THR B 235 2.06 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 36 CB - CA - C ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 135 CB - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 SER A 136 N - CA - CB ANGL. DEV. = -11.0 DEGREES REMARK 500 MET A 145 CB - CA - C ANGL. DEV. = 13.1 DEGREES REMARK 500 PHE A 324 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP B 36 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 135 CB - CA - C ANGL. DEV. = 17.6 DEGREES REMARK 500 SER B 136 N - CA - CB ANGL. DEV. = -11.8 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 LYS A 5 -5.07 -147.75 REMARK 500 TYR A 26 -72.41 -65.67 REMARK 500 LEU A 66 -72.03 -74.55 REMARK 500 LYS A 69 -70.48 -99.04 REMARK 500 ARG A 73 33.03 -92.93 REMARK 500 LYS A 74 6.13 54.62 REMARK 500 MET A 86 57.35 -99.99 REMARK 500 PRO A 89 12.52 -68.87 REMARK 500 ASN A 102 26.65 43.16 REMARK 500 ASN A 165 103.59 -162.42 REMARK 500 SER A 375 -74.82 -92.13 REMARK 500 LYS B 5 -4.09 -149.03 REMARK 500 TYR B 26 -72.30 -65.68 REMARK 500 LEU B 66 -72.29 -74.47 REMARK 500 LYS B 69 -73.65 -98.60 REMARK 500 MET B 86 57.16 -99.75 REMARK 500 PRO B 89 12.44 -68.88 REMARK 500 ASN B 102 -10.31 69.92 REMARK 500 ASN B 165 103.37 -162.33 REMARK 500 LEU B 178 -67.45 -90.98 REMARK 500 LYS B 188 -157.04 -104.38 REMARK 500 ALA B 353 -70.04 -93.59 REMARK 500 SER B 375 -74.81 -91.98 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 ARG A 144 0.18 SIDE CHAIN REMARK 500 ARG B 144 0.20 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 BA A 501 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 130 OE1 REMARK 620 2 GLU A 130 OE2 37.9 REMARK 620 3 ASN A 204 OD1 96.3 59.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 501 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 130 OE2 REMARK 620 2 GLU B 130 OE1 37.9 REMARK 620 3 ASN B 204 OD1 61.7 99.6 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PV6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LACTOSE PERMEASE REMARK 900 RELATED ID: 2V8N RELATED DB: PDB REMARK 900 WILD-TYPE STRUCTURE OF LACTOSE PERMEASE REMARK 900 RELATED ID: 1PV7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LACTOSE PERMEASE WITH TDG REMARK 900 RELATED ID: 2CFP RELATED DB: PDB REMARK 900 SUGAR FREE LACTOSE PERMEASE AT ACIDIC PH REMARK 900 RELATED ID: 2CFQ RELATED DB: PDB REMARK 900 SUGAR FREE LACTOSE PERMEASE AT NEUTRAL PH DBREF 2Y5Y A 1 417 UNP P02920 LACY_ECOLI 1 417 DBREF 2Y5Y B 1 417 UNP P02920 LACY_ECOLI 1 417 SEQADV 2Y5Y SER A 117 UNP P02920 CYS 117 ENGINEERED MUTATION SEQADV 2Y5Y CYS A 122 UNP P02920 ALA 122 ENGINEERED MUTATION SEQADV 2Y5Y ALA A 148 UNP P02920 CYS 148 ENGINEERED MUTATION SEQADV 2Y5Y VAL A 154 UNP P02920 CYS 154 ENGINEERED MUTATION SEQADV 2Y5Y MET A 176 UNP P02920 CYS 176 ENGINEERED MUTATION SEQADV 2Y5Y SER A 234 UNP P02920 CYS 234 ENGINEERED MUTATION SEQADV 2Y5Y SER A 333 UNP P02920 CYS 333 ENGINEERED MUTATION SEQADV 2Y5Y ALA A 353 UNP P02920 CYS 353 ENGINEERED MUTATION SEQADV 2Y5Y ALA A 355 UNP P02920 CYS 355 ENGINEERED MUTATION SEQADV 2Y5Y HIS A 418 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS A 419 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS A 420 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS A 421 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS A 422 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS A 423 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y SER B 117 UNP P02920 CYS 117 ENGINEERED MUTATION SEQADV 2Y5Y CYS B 122 UNP P02920 ALA 122 ENGINEERED MUTATION SEQADV 2Y5Y ALA B 148 UNP P02920 CYS 148 ENGINEERED MUTATION SEQADV 2Y5Y VAL B 154 UNP P02920 CYS 154 ENGINEERED MUTATION SEQADV 2Y5Y MET B 176 UNP P02920 CYS 176 ENGINEERED MUTATION SEQADV 2Y5Y SER B 234 UNP P02920 CYS 234 ENGINEERED MUTATION SEQADV 2Y5Y SER B 333 UNP P02920 CYS 333 ENGINEERED MUTATION SEQADV 2Y5Y ALA B 353 UNP P02920 CYS 353 ENGINEERED MUTATION SEQADV 2Y5Y ALA B 355 UNP P02920 CYS 355 ENGINEERED MUTATION SEQADV 2Y5Y HIS B 418 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS B 419 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS B 420 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS B 421 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS B 422 UNP P02920 EXPRESSION TAG SEQADV 2Y5Y HIS B 423 UNP P02920 EXPRESSION TAG SEQRES 1 A 423 MET TYR TYR LEU LYS ASN THR ASN PHE TRP MET PHE GLY SEQRES 2 A 423 LEU PHE PHE PHE PHE TYR PHE PHE ILE MET GLY ALA TYR SEQRES 3 A 423 PHE PRO PHE PHE PRO ILE TRP LEU HIS ASP ILE ASN HIS SEQRES 4 A 423 ILE SER LYS SER ASP THR GLY ILE ILE PHE ALA ALA ILE SEQRES 5 A 423 SER LEU PHE SER LEU LEU PHE GLN PRO LEU PHE GLY LEU SEQRES 6 A 423 LEU SER ASP LYS LEU GLY LEU ARG LYS TYR LEU LEU TRP SEQRES 7 A 423 ILE ILE THR GLY MET LEU VAL MET PHE ALA PRO PHE PHE SEQRES 8 A 423 ILE PHE ILE PHE GLY PRO LEU LEU GLN TYR ASN ILE LEU SEQRES 9 A 423 VAL GLY SER ILE VAL GLY GLY ILE TYR LEU GLY PHE SER SEQRES 10 A 423 PHE ASN ALA GLY CYS PRO ALA VAL GLU ALA PHE ILE GLU SEQRES 11 A 423 LYS VAL SER ARG ARG SER ASN PHE GLU PHE GLY ARG ALA SEQRES 12 A 423 ARG MET PHE GLY ALA VAL GLY TRP ALA LEU VAL ALA SER SEQRES 13 A 423 ILE VAL GLY ILE MET PHE THR ILE ASN ASN GLN PHE VAL SEQRES 14 A 423 PHE TRP LEU GLY SER GLY MET ALA LEU ILE LEU ALA VAL SEQRES 15 A 423 LEU LEU PHE PHE ALA LYS THR ASP ALA PRO SER SER ALA SEQRES 16 A 423 THR VAL ALA ASN ALA VAL GLY ALA ASN HIS SER ALA PHE SEQRES 17 A 423 SER LEU LYS LEU ALA LEU GLU LEU PHE ARG GLN PRO LYS SEQRES 18 A 423 LEU TRP PHE LEU SER LEU TYR VAL ILE GLY VAL SER SER SEQRES 19 A 423 THR TYR ASP VAL PHE ASP GLN GLN PHE ALA ASN PHE PHE SEQRES 20 A 423 THR SER PHE PHE ALA THR GLY GLU GLN GLY THR ARG VAL SEQRES 21 A 423 PHE GLY TYR VAL THR THR MET GLY GLU LEU LEU ASN ALA SEQRES 22 A 423 SER ILE MET PHE PHE ALA PRO LEU ILE ILE ASN ARG ILE SEQRES 23 A 423 GLY GLY LYS ASN ALA LEU LEU LEU ALA GLY THR ILE MET SEQRES 24 A 423 SER VAL ARG ILE ILE GLY SER SER PHE ALA THR SER ALA SEQRES 25 A 423 LEU GLU VAL VAL ILE LEU LYS THR LEU HIS MET PHE GLU SEQRES 26 A 423 VAL PRO PHE LEU LEU VAL GLY SER PHE LYS TYR ILE THR SEQRES 27 A 423 SER GLN PHE GLU VAL ARG PHE SER ALA THR ILE TYR LEU SEQRES 28 A 423 VAL ALA PHE ALA PHE PHE LYS GLN LEU ALA MET ILE PHE SEQRES 29 A 423 MET SER VAL LEU ALA GLY ASN MET TYR GLU SER ILE GLY SEQRES 30 A 423 PHE GLN GLY ALA TYR LEU VAL LEU GLY LEU VAL ALA LEU SEQRES 31 A 423 GLY PHE THR LEU ILE SER VAL PHE THR LEU SER GLY PRO SEQRES 32 A 423 GLY PRO LEU SER LEU LEU ARG ARG GLN VAL ASN GLU VAL SEQRES 33 A 423 ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 423 MET TYR TYR LEU LYS ASN THR ASN PHE TRP MET PHE GLY SEQRES 2 B 423 LEU PHE PHE PHE PHE TYR PHE PHE ILE MET GLY ALA TYR SEQRES 3 B 423 PHE PRO PHE PHE PRO ILE TRP LEU HIS ASP ILE ASN HIS SEQRES 4 B 423 ILE SER LYS SER ASP THR GLY ILE ILE PHE ALA ALA ILE SEQRES 5 B 423 SER LEU PHE SER LEU LEU PHE GLN PRO LEU PHE GLY LEU SEQRES 6 B 423 LEU SER ASP LYS LEU GLY LEU ARG LYS TYR LEU LEU TRP SEQRES 7 B 423 ILE ILE THR GLY MET LEU VAL MET PHE ALA PRO PHE PHE SEQRES 8 B 423 ILE PHE ILE PHE GLY PRO LEU LEU GLN TYR ASN ILE LEU SEQRES 9 B 423 VAL GLY SER ILE VAL GLY GLY ILE TYR LEU GLY PHE SER SEQRES 10 B 423 PHE ASN ALA GLY CYS PRO ALA VAL GLU ALA PHE ILE GLU SEQRES 11 B 423 LYS VAL SER ARG ARG SER ASN PHE GLU PHE GLY ARG ALA SEQRES 12 B 423 ARG MET PHE GLY ALA VAL GLY TRP ALA LEU VAL ALA SER SEQRES 13 B 423 ILE VAL GLY ILE MET PHE THR ILE ASN ASN GLN PHE VAL SEQRES 14 B 423 PHE TRP LEU GLY SER GLY MET ALA LEU ILE LEU ALA VAL SEQRES 15 B 423 LEU LEU PHE PHE ALA LYS THR ASP ALA PRO SER SER ALA SEQRES 16 B 423 THR VAL ALA ASN ALA VAL GLY ALA ASN HIS SER ALA PHE SEQRES 17 B 423 SER LEU LYS LEU ALA LEU GLU LEU PHE ARG GLN PRO LYS SEQRES 18 B 423 LEU TRP PHE LEU SER LEU TYR VAL ILE GLY VAL SER SER SEQRES 19 B 423 THR TYR ASP VAL PHE ASP GLN GLN PHE ALA ASN PHE PHE SEQRES 20 B 423 THR SER PHE PHE ALA THR GLY GLU GLN GLY THR ARG VAL SEQRES 21 B 423 PHE GLY TYR VAL THR THR MET GLY GLU LEU LEU ASN ALA SEQRES 22 B 423 SER ILE MET PHE PHE ALA PRO LEU ILE ILE ASN ARG ILE SEQRES 23 B 423 GLY GLY LYS ASN ALA LEU LEU LEU ALA GLY THR ILE MET SEQRES 24 B 423 SER VAL ARG ILE ILE GLY SER SER PHE ALA THR SER ALA SEQRES 25 B 423 LEU GLU VAL VAL ILE LEU LYS THR LEU HIS MET PHE GLU SEQRES 26 B 423 VAL PRO PHE LEU LEU VAL GLY SER PHE LYS TYR ILE THR SEQRES 27 B 423 SER GLN PHE GLU VAL ARG PHE SER ALA THR ILE TYR LEU SEQRES 28 B 423 VAL ALA PHE ALA PHE PHE LYS GLN LEU ALA MET ILE PHE SEQRES 29 B 423 MET SER VAL LEU ALA GLY ASN MET TYR GLU SER ILE GLY SEQRES 30 B 423 PHE GLN GLY ALA TYR LEU VAL LEU GLY LEU VAL ALA LEU SEQRES 31 B 423 GLY PHE THR LEU ILE SER VAL PHE THR LEU SER GLY PRO SEQRES 32 B 423 GLY PRO LEU SER LEU LEU ARG ARG GLN VAL ASN GLU VAL SEQRES 33 B 423 ALA HIS HIS HIS HIS HIS HIS HET BA A 501 1 HET TGA A 701 15 HET BA B 501 1 HET TGA B 801 15 HETNAM BA BARIUM ION HETNAM TGA 2-SULFANYLETHYL BETA-D-GALACTOPYRANOSIDE HETSYN TGA METHANETHIOSULFONYL-GALACTOSIDE; 2-SULFANYLETHYL BETA- HETSYN 2 TGA D-GALACTOSIDE; 2-SULFANYLETHYL D-GALACTOSIDE; 2- HETSYN 3 TGA SULFANYLETHYL GALACTOSIDE FORMUL 3 BA 2(BA 2+) FORMUL 4 TGA 2(C8 H16 O6 S) HELIX 1 1 ASN A 6 PHE A 27 1 22 HELIX 2 2 PHE A 29 ASP A 36 1 8 HELIX 3 3 SER A 41 LEU A 70 1 30 HELIX 4 4 GLY A 71 ARG A 73 5 3 HELIX 5 5 LYS A 74 MET A 86 1 13 HELIX 6 6 PHE A 87 ILE A 92 1 6 HELIX 7 7 ILE A 94 TYR A 101 1 8 HELIX 8 8 ILE A 103 SER A 136 1 34 HELIX 9 9 GLU A 139 ILE A 179 1 41 HELIX 10 10 VAL A 182 ALA A 187 1 6 HELIX 11 11 SER A 209 GLN A 219 1 11 HELIX 12 12 GLN A 219 VAL A 232 1 14 HELIX 13 13 VAL A 232 GLN A 242 1 11 HELIX 14 14 GLN A 242 PHE A 250 1 9 HELIX 15 15 THR A 253 SER A 307 1 55 HELIX 16 16 SER A 311 PHE A 341 1 31 HELIX 17 17 GLU A 342 ARG A 344 5 3 HELIX 18 18 PHE A 345 ALA A 353 1 9 HELIX 19 19 ALA A 355 ILE A 376 1 22 HELIX 20 20 ILE A 376 LEU A 400 1 25 HELIX 21 21 ASN B 6 PHE B 27 1 22 HELIX 22 22 PHE B 29 ASP B 36 1 8 HELIX 23 23 SER B 41 LEU B 70 1 30 HELIX 24 24 GLY B 71 ARG B 73 5 3 HELIX 25 25 LYS B 74 MET B 86 1 13 HELIX 26 26 PHE B 87 ILE B 92 1 6 HELIX 27 27 ILE B 94 TYR B 101 1 8 HELIX 28 28 ILE B 103 TYR B 113 1 11 HELIX 29 29 GLY B 115 ALA B 120 1 6 HELIX 30 30 ALA B 120 SER B 136 1 17 HELIX 31 31 GLU B 139 ILE B 179 1 41 HELIX 32 32 LEU B 180 ALA B 187 1 8 HELIX 33 33 SER B 209 GLN B 219 1 11 HELIX 34 34 GLN B 219 VAL B 232 1 14 HELIX 35 35 VAL B 232 GLN B 242 1 11 HELIX 36 36 GLN B 242 PHE B 250 1 9 HELIX 37 37 THR B 253 SER B 307 1 55 HELIX 38 38 SER B 311 PHE B 341 1 31 HELIX 39 39 GLU B 342 ARG B 344 5 3 HELIX 40 40 PHE B 345 ALA B 353 1 9 HELIX 41 41 PHE B 356 ILE B 376 1 21 HELIX 42 42 ILE B 376 SER B 396 1 21 HELIX 43 43 VAL B 397 THR B 399 5 3 LINK SG CYS A 122 S15 TGA A 701 1555 1555 2.08 LINK SG CYS B 122 S15 TGA B 801 1555 1555 2.06 LINK OE1 GLU A 130 BA BA A 501 1555 1555 3.42 LINK OE2 GLU A 130 BA BA A 501 1555 1555 3.37 LINK OD1 ASN A 204 BA BA A 501 1555 1555 3.14 LINK OE2 GLU B 130 BA BA B 501 1555 1555 3.37 LINK OE1 GLU B 130 BA BA B 501 1555 1555 3.42 LINK OD1 ASN B 204 BA BA B 501 1555 1555 3.01 CRYST1 102.560 127.840 189.870 90.00 90.00 90.00 P 21 21 21 8 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 0.009750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005267 0.00000