HEADER TRANSPORT PROTEIN 02-OCT-09 3K3G TITLE CRYSTAL STRUCTURE OF THE UREA TRANSPORTER FROM DESULFOVIBRIO VULGARIS TITLE 2 BOUND TO 1,3-DIMETHYLUREA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UREA TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 882; SOURCE 4 STRAIN: HILDENBOROUGH; SOURCE 5 GENE: DVU_1160; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS MEMBRANE PROTEIN, CHANNEL, UREA TRANSPORT, TRANSPORTER, TRANSPORT KEYWDS 2 PROTEIN, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 NEW YORK CONSORTIUM ON MEMBRANE PROTEIN STRUCTURE, NYCOMPS EXPDTA X-RAY DIFFRACTION AUTHOR E.J.LEVIN,M.ZHOU,NEW YORK CONSORTIUM ON MEMBRANE PROTEIN STRUCTURE AUTHOR 2 (NYCOMPS) REVDAT 5 06-SEP-23 3K3G 1 REMARK SEQADV LINK REVDAT 4 01-NOV-17 3K3G 1 REMARK REVDAT 3 13-JUL-11 3K3G 1 VERSN REVDAT 2 15-DEC-09 3K3G 1 JRNL REVDAT 1 17-NOV-09 3K3G 0 JRNL AUTH E.J.LEVIN,M.QUICK,M.ZHOU JRNL TITL CRYSTAL STRUCTURE OF A BACTERIAL HOMOLOGUE OF THE KIDNEY JRNL TITL 2 UREA TRANSPORTER. JRNL REF NATURE V. 462 757 2009 JRNL REFN ISSN 0028-0836 JRNL PMID 19865084 JRNL DOI 10.1038/NATURE08558 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 22964 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1166 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1573 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.33 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2481 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 28 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) : 44.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -0.67000 REMARK 3 B12 (A**2) : 0.22000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.211 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.178 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2554 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3476 ; 1.338 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 329 ; 5.490 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;39.846 ;22.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 386 ;15.737 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.680 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 414 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1891 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1316 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1807 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 88 ; 0.126 ; 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): 85 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.112 ; 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): 1681 ; 0.559 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2621 ; 0.985 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1005 ; 1.468 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 855 ; 2.101 ; 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 : 4 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 0 A 15 REMARK 3 ORIGIN FOR THE GROUP (A): 60.6756 5.3778 -18.4165 REMARK 3 T TENSOR REMARK 3 T11: 0.4279 T22: 0.0337 REMARK 3 T33: 0.3171 T12: 0.0681 REMARK 3 T13: 0.0709 T23: 0.3571 REMARK 3 L TENSOR REMARK 3 L11: 4.8342 L22: 7.9641 REMARK 3 L33: 30.1202 L12: -1.6929 REMARK 3 L13: 9.0620 L23: -13.0124 REMARK 3 S TENSOR REMARK 3 S11: -0.6349 S12: -0.3058 S13: 0.0239 REMARK 3 S21: 0.2416 S22: -0.7059 S23: -0.7600 REMARK 3 S31: 0.2275 S32: -0.0217 S33: 1.3408 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 16 A 181 REMARK 3 ORIGIN FOR THE GROUP (A): 56.3248 -11.1229 2.1456 REMARK 3 T TENSOR REMARK 3 T11: 0.2863 T22: 0.0628 REMARK 3 T33: 0.2399 T12: -0.0059 REMARK 3 T13: -0.1542 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 2.1977 L22: 1.9980 REMARK 3 L33: 1.5486 L12: 0.1097 REMARK 3 L13: -0.1939 L23: -0.2546 REMARK 3 S TENSOR REMARK 3 S11: -0.1533 S12: 0.0243 S13: 0.6072 REMARK 3 S21: 0.0216 S22: -0.2017 S23: -0.0641 REMARK 3 S31: -0.4442 S32: 0.0300 S33: 0.3550 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 182 A 312 REMARK 3 ORIGIN FOR THE GROUP (A): 40.8581 -15.2346 1.3617 REMARK 3 T TENSOR REMARK 3 T11: 0.1942 T22: 0.1491 REMARK 3 T33: 0.2654 T12: 0.0919 REMARK 3 T13: -0.1427 T23: -0.0898 REMARK 3 L TENSOR REMARK 3 L11: 1.6366 L22: 1.5598 REMARK 3 L33: 1.6575 L12: 0.1748 REMARK 3 L13: 0.0048 L23: -0.0848 REMARK 3 S TENSOR REMARK 3 S11: -0.1411 S12: 0.0979 S13: 0.4876 REMARK 3 S21: -0.0226 S22: -0.1741 S23: 0.4281 REMARK 3 S31: -0.3122 S32: -0.3262 S33: 0.3152 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 : A 313 A 334 REMARK 3 ORIGIN FOR THE GROUP (A): 39.4900 -12.7689 -19.0106 REMARK 3 T TENSOR REMARK 3 T11: 0.2869 T22: 0.2386 REMARK 3 T33: -0.0502 T12: 0.1595 REMARK 3 T13: -0.4200 T23: 0.1160 REMARK 3 L TENSOR REMARK 3 L11: 9.7948 L22: 19.0035 REMARK 3 L33: 8.0071 L12: 2.1701 REMARK 3 L13: -2.3286 L23: -2.3764 REMARK 3 S TENSOR REMARK 3 S11: -0.1669 S12: 1.0377 S13: 0.7335 REMARK 3 S21: -2.5393 S22: 0.0064 S23: -0.5474 REMARK 3 S31: -0.3537 S32: 0.0066 S33: 0.1605 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3K3G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) 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 : 22979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.91500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3K3F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 1500, 100 MM NA CACODYLATE, 10 REMARK 280 MM N,N'-DIMETHYLUREA, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.43600 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 42.43600 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 42.43600 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 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 -0.500000 -0.866025 0.000000 55.05300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -95.35459 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 110.10600 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 SER A -2 REMARK 465 GLY A -1 REMARK 465 ALA A 164 REMARK 465 GLY A 165 REMARK 465 LEU A 166 REMARK 465 ALA A 167 REMARK 465 GLY A 335 REMARK 465 SER A 336 REMARK 465 ARG A 337 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 CYS A 224 CB CYS A 224 SG 0.265 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 LEU A 329 CB - CG - CD2 ANGL. DEV. = 14.3 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 ALA A 1 118.19 -36.73 REMARK 500 LEU A 129 -142.95 52.80 REMARK 500 ASN A 193 115.84 -160.09 REMARK 500 LEU A 293 -133.71 55.07 REMARK 500 ALA A 322 106.69 -51.64 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 AU A 340 AU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 O REMARK 620 2 CYS A 15 SG 81.7 REMARK 620 3 CYS A 19 SG 108.2 165.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 342 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AU A 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMU A 347 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MMU A 348 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K3F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UREA TRANSPORTER FROM DESULFOVIBRIO REMARK 900 VULGARIS REMARK 900 RELATED ID: GO.3782 RELATED DB: TARGETDB DBREF 3K3G A 2 337 UNP Q72CX3 Q72CX3_DESVH 2 337 SEQADV 3K3G SER A -2 UNP Q72CX3 EXPRESSION TAG SEQADV 3K3G GLY A -1 UNP Q72CX3 EXPRESSION TAG SEQADV 3K3G ARG A 0 UNP Q72CX3 EXPRESSION TAG SEQADV 3K3G ALA A 1 UNP Q72CX3 EXPRESSION TAG SEQRES 1 A 340 SER GLY ARG ALA PHE GLY GLU GLN LEU LEU LYS ASN PRO SEQRES 2 A 340 LEU ILE GLU PHE CYS ASP SER VAL CYS ARG GLY CYS GLY SEQRES 3 A 340 GLN VAL MET PHE GLN ASN ASN THR VAL THR GLY LEU LEU SEQRES 4 A 340 PHE PHE ALA GLY ILE PHE TYR ASN SER THR THR LEU GLY SEQRES 5 A 340 VAL CYS ALA VAL LEU GLY THR ALA ALA SER THR LEU THR SEQRES 6 A 340 ALA GLN LEU LEU GLY VAL ASP LYS PRO LEU VAL ARG ALA SEQRES 7 A 340 GLY LEU PHE GLY PHE ASN GLY THR LEU ALA GLY ILE ALA SEQRES 8 A 340 LEU PRO PHE PHE PHE ASN TYR GLU PRO ALA MET LEU GLY SEQRES 9 A 340 TYR VAL ALA LEU ASN GLY ALA PHE THR THR ILE ILE MET SEQRES 10 A 340 ALA SER LEU LEU ASN PHE LEU GLY LYS TRP GLY VAL PRO SEQRES 11 A 340 ALA LEU THR ALA PRO PHE VAL LEU ALA THR TRP LEU LEU SEQRES 12 A 340 MET PHE GLY VAL TYR LYS LEU SER LEU PHE HIS PRO GLY SEQRES 13 A 340 ALA LEU ILE ALA PRO ALA LEU PRO SER VAL ALA GLY LEU SEQRES 14 A 340 ALA ASP MET GLY THR VAL THR GLY ARG THR PHE MET GLU SEQRES 15 A 340 GLY LEU PHE LYS GLY VAL GLY GLU VAL MET PHE GLN ASP SEQRES 16 A 340 ASN ILE VAL THR GLY VAL ILE PHE VAL VAL ALA ILE LEU SEQRES 17 A 340 VAL ASN SER ARG ILE SER ALA LEU PHE ALA VAL ILE GLY SEQRES 18 A 340 SER LEU VAL GLY LEU CYS THR ALA LEU ILE MET HIS SER SEQRES 19 A 340 PRO GLU THR PRO VAL ARG LEU GLY LEU TYR GLY PHE ASN SEQRES 20 A 340 SER VAL LEU CYS GLY ILE ALA MET GLY GLY ILE PHE PHE SEQRES 21 A 340 TYR LEU ASN ILE ARG THR PHE LEU TYR ALA LEU GLY CYS SEQRES 22 A 340 MET VAL LEU GLY ALA ILE ALA THR GLY ALA PHE SER VAL SEQRES 23 A 340 LEU LEU SER PRO ILE GLY MET PRO ALA LEU THR TRP PRO SEQRES 24 A 340 PHE ILE VAL VAL THR TRP LEU PHE LEU PHE ALA GLY SER SEQRES 25 A 340 MET PHE ARG ASN ILE ALA GLN VAL PRO THR GLU LYS ALA SEQRES 26 A 340 GLY THR PRO GLU ASP ASN LEU ARG SER LEU ALA ILE GLY SEQRES 27 A 340 SER ARG HET AU A 338 1 HET AU A 339 1 HET AU A 340 1 HET AU A 341 1 HET AU A 342 1 HET AU A 343 1 HET AU A 344 1 HET AU A 345 1 HET AU A 346 1 HET MMU A 347 6 HET MMU A 348 6 HETNAM AU GOLD ION HETNAM MMU 1,3-DIMETHYLUREA FORMUL 2 AU 9(AU 1+) FORMUL 11 MMU 2(C3 H8 N2 O) FORMUL 13 HOH *28(H2 O) HELIX 1 1 ALA A 1 LYS A 8 5 8 HELIX 2 2 ASN A 9 GLN A 24 1 16 HELIX 3 3 VAL A 25 PHE A 27 5 3 HELIX 4 4 ASN A 30 SER A 45 1 16 HELIX 5 5 SER A 45 GLY A 67 1 23 HELIX 6 6 ASP A 69 ALA A 75 1 7 HELIX 7 7 GLY A 79 PHE A 93 1 15 HELIX 8 8 ALA A 98 GLY A 122 1 25 HELIX 9 9 LYS A 123 GLY A 125 5 3 HELIX 10 10 THR A 130 PHE A 142 1 13 HELIX 11 11 GLY A 143 LYS A 146 5 4 HELIX 12 12 THR A 173 GLU A 187 1 15 HELIX 13 13 VAL A 188 PHE A 190 5 3 HELIX 14 14 ASN A 193 SER A 208 1 16 HELIX 15 15 SER A 208 MET A 229 1 22 HELIX 16 16 PRO A 232 LEU A 238 1 7 HELIX 17 17 GLY A 242 GLY A 253 1 12 HELIX 18 18 ASN A 260 LEU A 285 1 26 HELIX 19 19 SER A 286 GLY A 289 5 4 HELIX 20 20 THR A 294 GLY A 308 1 15 HELIX 21 21 SER A 309 PHE A 311 5 3 HELIX 22 22 THR A 324 ALA A 333 1 10 SSBOND 1 CYS A 248 CYS A 270 1555 1555 2.29 LINK O CYS A 15 AU AU A 340 1555 1555 2.15 LINK SG CYS A 15 AU AU A 340 1555 1555 2.87 LINK SG CYS A 15 AU AU A 342 1555 1555 1.89 LINK SG CYS A 19 AU AU A 339 1555 1555 2.69 LINK SG CYS A 19 AU AU A 340 1555 1555 2.41 LINK SG CYS A 51 AU AU A 343 1555 1555 2.79 LINK SG CYS A 51 AU AU A 344 1555 1555 2.37 LINK SG CYS A 224 AU AU A 345 1555 1555 2.59 LINK SG CYS A 224 AU AU A 346 1555 1555 1.73 SITE 1 AC1 1 GLN A 24 SITE 1 AC2 5 CYS A 19 THR A 31 LEU A 35 AU A 340 SITE 2 AC2 5 AU A 341 SITE 1 AC3 5 CYS A 15 CYS A 19 AU A 339 AU A 341 SITE 2 AC3 5 AU A 342 SITE 1 AC4 5 CYS A 15 ASP A 16 AU A 339 AU A 340 SITE 2 AC4 5 AU A 342 SITE 1 AC5 3 CYS A 15 AU A 340 AU A 341 SITE 1 AC6 4 THR A 47 VAL A 50 CYS A 51 AU A 344 SITE 1 AC7 3 THR A 47 CYS A 51 AU A 343 SITE 1 AC8 2 CYS A 224 AU A 346 SITE 1 AC9 2 CYS A 224 AU A 345 SITE 1 BC1 5 GLU A 187 VAL A 188 PHE A 190 PHE A 243 SITE 2 BC1 5 HOH A 359 SITE 1 BC2 8 GLN A 24 VAL A 25 PHE A 27 LEU A 77 SITE 2 BC2 8 PHE A 80 LEU A 129 THR A 130 HOH A 370 CRYST1 110.106 110.106 84.872 90.00 90.00 120.00 P 63 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 0.009082 0.005244 0.000000 0.00000 SCALE2 0.000000 0.010487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011782 0.00000