HEADER MEMBRANE PROTEIN 27-APR-10 3MPV TITLE STRUCTURE OF EUTL IN THE ZINC-INDUCED OPEN FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ETHANOLAMINE UTILIZATION PROTEIN EUTL; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2439, EUTL, JW2432, YFFJ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: TOPO101 KEYWDS SHELL PROTEIN, BACTERIAL MICROCOMPARTMENT, ETHANOLAMINE, CARBOXYSOME, KEYWDS 2 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SAGERMANN,M.TAKENOYA,K.NIKOLAKAKIS REVDAT 3 06-SEP-23 3MPV 1 REMARK SEQADV LINK REVDAT 2 20-JUN-12 3MPV 1 JRNL VERSN REVDAT 1 22-SEP-10 3MPV 0 JRNL AUTH M.TAKENOYA,K.NIKOLAKAKIS,M.SAGERMANN JRNL TITL CRYSTALLOGRAPHIC INSIGHTS INTO THE PORE STRUCTURES AND JRNL TITL 2 MECHANISMS OF THE EUTL AND EUTM SHELL PROTEINS OF THE JRNL TITL 3 ETHANOLAMINE-UTILIZING MICROCOMPARTMENT OF ESCHERICHIA COLI. JRNL REF J.BACTERIOL. V. 192 6056 2010 JRNL REFN ISSN 0021-9193 JRNL PMID 20851901 JRNL DOI 10.1128/JB.00652-10 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.SAGERMANN,A.OHTAKI,K.NIKOLAKAKIS REMARK 1 TITL CRYSTAL STRUCTURE OF THE EUTL SHELL PROTEIN OF THE REMARK 1 TITL 2 ETHANOLAMINE AMMONIA LYASE MICROCOMPARTMENT. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 106 8883 2009 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 19451619 REMARK 1 DOI 10.1073/PNAS.0902324106 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 11250 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.900 REMARK 3 FREE R VALUE TEST SET COUNT : 972 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 789 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.4520 REMARK 3 BIN FREE R VALUE SET COUNT : 74 REMARK 3 BIN FREE R VALUE : 0.4700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2942 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 13 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -34.58000 REMARK 3 B22 (A**2) : -34.58000 REMARK 3 B33 (A**2) : 69.17000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.291 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.419 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.904 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.850 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2999 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2803 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4096 ; 2.171 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6483 ; 0.866 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 394 ; 7.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;39.957 ;24.386 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 442 ;22.780 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.345 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3364 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 562 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1998 ; 0.808 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 808 ; 0.144 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3196 ; 1.480 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1001 ; 2.230 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 900 ; 3.633 ; 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 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.550 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : K, H, -L REMARK 3 TWIN FRACTION : 0.450 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DATA SETS FOR REMARK 3 THIS CRYSTAL APPEARED TWINNED. REFINEMENT WAS CARRIED OUT AS REMARK 3 DESCRIBED IN PRIMARY CITATION. REMARK 3 THE N-TERMINAL METHIONINE AS WELL AS THE RESIDUES FROM 215B (OR REMARK 3 216A) ON (INCLUDING THE HIS6-TAG) WERE NOT VISIBLE IN THE DENSITY. REMARK 3 LIKEWISE, THE AAS BETWEEN RESIDUES 69 AND 83 AND 180-183 WERE ALSO REMARK 3 NOT VISIBLE IN THE DENSITY. REMARK 4 REMARK 4 3MPV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-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 : 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) : 0.979464 REMARK 200 MONOCHROMATOR : SI 111 BEND CRYSTAL REMARK 200 OPTICS : SI III 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 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11274 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 58.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.11700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 1.9000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3GFH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M NACL, 100 MM PHOSPHATE, 100 MM MES REMARK 280 BUFFER, 5 % PEG 400, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -428.0 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 101.12250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 58.38310 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 116.76621 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -215.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 BIOMT1 2 -0.500000 -0.866025 0.000000 101.12250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 58.38310 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 116.76621 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 MET A 1 REMARK 465 TYR A 70 REMARK 465 ALA A 71 REMARK 465 GLY A 72 REMARK 465 ALA A 73 REMARK 465 ALA A 74 REMARK 465 HIS A 75 REMARK 465 GLY A 76 REMARK 465 PRO A 77 REMARK 465 SER A 78 REMARK 465 PRO A 79 REMARK 465 THR A 80 REMARK 465 ALA A 81 REMARK 465 GLY A 82 REMARK 465 SER A 181 REMARK 465 GLU A 182 REMARK 465 GLN A 217 REMARK 465 ARG A 218 REMARK 465 ALA A 219 REMARK 465 HIS A 220 REMARK 465 HIS A 221 REMARK 465 HIS A 222 REMARK 465 HIS A 223 REMARK 465 HIS A 224 REMARK 465 HIS A 225 REMARK 465 MET B 1 REMARK 465 TYR B 70 REMARK 465 ALA B 71 REMARK 465 GLY B 72 REMARK 465 ALA B 73 REMARK 465 ALA B 74 REMARK 465 HIS B 75 REMARK 465 GLY B 76 REMARK 465 PRO B 77 REMARK 465 SER B 78 REMARK 465 PRO B 79 REMARK 465 THR B 80 REMARK 465 ALA B 81 REMARK 465 GLY B 82 REMARK 465 SER B 181 REMARK 465 GLU B 182 REMARK 465 GLN B 217 REMARK 465 ARG B 218 REMARK 465 ALA B 219 REMARK 465 HIS B 220 REMARK 465 HIS B 221 REMARK 465 HIS B 222 REMARK 465 HIS B 223 REMARK 465 HIS B 224 REMARK 465 HIS B 225 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 OE2 GLU A 157 ZN ZN A 903 1.58 REMARK 500 O ASN B 214 N ILE B 216 1.67 REMARK 500 O ALA B 207 CD1 ILE B 211 1.80 REMARK 500 CG MET B 60 O HOH B 228 1.88 REMARK 500 OD2 ASP B 23 O HOH B 229 1.89 REMARK 500 CE1 HIS A 106 O HOH A 228 1.96 REMARK 500 CB CYS A 201 S2 BME A 226 2.00 REMARK 500 CE1 HIS B 106 O HOH B 227 2.01 REMARK 500 OD1 ASP A 23 NH2 ARG A 26 2.09 REMARK 500 O ASP B 43 CB GLU B 83 2.09 REMARK 500 SG CYS A 201 S2 BME A 226 2.10 REMARK 500 O ALA B 165 OG SER B 168 2.11 REMARK 500 OE1 GLU A 62 OG SER A 134 2.12 REMARK 500 N MET B 60 OE2 GLU B 95 2.13 REMARK 500 OG1 THR A 143 OD2 ASP A 146 2.16 REMARK 500 O ALA B 140 N ILE B 142 2.17 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 NH2 ARG B 15 CG1 ILE B 211 3665 1.79 REMARK 500 NH2 ARG A 15 CD1 ILE A 211 2665 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU B 62 CB GLU B 62 CG 0.134 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 PRO B 9 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO B 179 C - N - CD ANGL. DEV. = -12.6 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 3 -85.10 -79.25 REMARK 500 ARG A 8 118.59 -21.01 REMARK 500 ARG A 15 133.91 -174.10 REMARK 500 ARG A 26 -76.48 -66.40 REMARK 500 LYS A 29 69.51 65.69 REMARK 500 ASP A 43 -67.18 -100.02 REMARK 500 TYR A 49 -49.18 -21.60 REMARK 500 THR A 56 4.40 -60.53 REMARK 500 MET A 60 86.17 -69.45 REMARK 500 TYR A 65 165.11 176.27 REMARK 500 LEU A 85 133.07 -172.59 REMARK 500 ASN A 109 81.23 -162.49 REMARK 500 PHE A 113 -179.58 -67.95 REMARK 500 ASP A 121 7.43 -155.48 REMARK 500 LEU A 125 103.19 -160.80 REMARK 500 THR A 139 41.04 -84.29 REMARK 500 ALA A 140 112.39 -179.03 REMARK 500 PRO A 147 -179.34 -58.77 REMARK 500 MET A 148 149.12 -176.65 REMARK 500 PRO A 155 -70.95 -33.04 REMARK 500 ASP A 170 96.24 -59.98 REMARK 500 THR A 175 133.12 171.22 REMARK 500 TYR A 176 93.21 -173.25 REMARK 500 SER A 193 -158.13 -69.98 REMARK 500 ALA A 199 -73.42 -48.35 REMARK 500 ALA A 200 -40.27 -22.73 REMARK 500 ALA A 207 -65.86 -28.94 REMARK 500 ASN A 214 -36.96 -135.26 REMARK 500 ALA B 3 -49.90 -22.39 REMARK 500 LEU B 4 21.83 -147.86 REMARK 500 LEU B 6 171.04 -51.83 REMARK 500 VAL B 11 111.81 -39.06 REMARK 500 ALA B 13 148.05 -179.98 REMARK 500 SER B 19 94.24 -162.96 REMARK 500 LEU B 37 131.24 -177.51 REMARK 500 ASP B 43 -70.84 -83.72 REMARK 500 ALA B 51 -24.46 -39.31 REMARK 500 VAL B 63 105.51 -55.07 REMARK 500 ALA B 98 -7.70 -55.69 REMARK 500 ILE B 107 -68.33 -94.37 REMARK 500 GLU B 108 -15.28 -45.87 REMARK 500 ASN B 109 24.85 -151.91 REMARK 500 ALA B 111 163.44 -39.92 REMARK 500 ALA B 112 135.02 -175.81 REMARK 500 PHE B 113 173.62 -57.52 REMARK 500 GLN B 120 14.78 44.07 REMARK 500 ALA B 126 69.68 -164.01 REMARK 500 ALA B 153 167.31 172.19 REMARK 500 PRO B 155 -86.40 -36.40 REMARK 500 LEU B 173 170.96 -58.33 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. 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 TYR A 176 VAL A 177 146.73 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 ZN A 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 127 ND1 REMARK 620 2 BME A 226 O1 119.3 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 226 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GFH RELATED DB: PDB REMARK 900 STRUCTURE OF EUTL IN THE "CLOSED FORM". IN CONTRAST TO THE NEW REMARK 900 STRUCTURE, 3GFH STILL EXHIBITS THREE SMALL PORES. REMARK 900 RELATED ID: 3MPW RELATED DB: PDB REMARK 900 RELATED ID: 3MPY RELATED DB: PDB DBREF 3MPV A 1 219 UNP P76541 EUTL_ECOLI 1 219 DBREF 3MPV B 1 219 UNP P76541 EUTL_ECOLI 1 219 SEQADV 3MPV HIS A 220 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS A 221 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS A 222 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS A 223 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS A 224 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS A 225 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 220 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 221 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 222 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 223 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 224 UNP P76541 EXPRESSION TAG SEQADV 3MPV HIS B 225 UNP P76541 EXPRESSION TAG SEQRES 1 A 225 MET PRO ALA LEU ASP LEU ILE ARG PRO SER VAL THR ALA SEQRES 2 A 225 MET ARG VAL ILE ALA SER VAL ASN ALA ASP PHE ALA ARG SEQRES 3 A 225 GLU LEU LYS LEU PRO PRO HIS ILE ARG SER LEU GLY LEU SEQRES 4 A 225 ILE SER ALA ASP SER ASP ASP VAL THR TYR ILE ALA ALA SEQRES 5 A 225 ASP GLU ALA THR LYS GLN ALA MET VAL GLU VAL VAL TYR SEQRES 6 A 225 GLY ARG SER LEU TYR ALA GLY ALA ALA HIS GLY PRO SER SEQRES 7 A 225 PRO THR ALA GLY GLU VAL LEU ILE MET LEU GLY GLY PRO SEQRES 8 A 225 ASN PRO ALA GLU VAL ARG ALA GLY LEU ASP ALA MET ILE SEQRES 9 A 225 ALA HIS ILE GLU ASN GLY ALA ALA PHE GLN TRP ALA ASN SEQRES 10 A 225 ASP ALA GLN ASP THR ALA PHE LEU ALA HIS VAL VAL SER SEQRES 11 A 225 ARG THR GLY SER TYR LEU SER SER THR ALA GLY ILE THR SEQRES 12 A 225 LEU GLY ASP PRO MET ALA TYR LEU VAL ALA PRO PRO LEU SEQRES 13 A 225 GLU ALA THR TYR GLY ILE ASP ALA ALA LEU LYS SER ALA SEQRES 14 A 225 ASP VAL GLN LEU ALA THR TYR VAL PRO PRO PRO SER GLU SEQRES 15 A 225 THR ASN TYR SER ALA ALA PHE LEU THR GLY SER GLN ALA SEQRES 16 A 225 ALA CYS LYS ALA ALA CYS ASN ALA PHE THR ASP ALA VAL SEQRES 17 A 225 LEU GLU ILE ALA ARG ASN PRO ILE GLN ARG ALA HIS HIS SEQRES 18 A 225 HIS HIS HIS HIS SEQRES 1 B 225 MET PRO ALA LEU ASP LEU ILE ARG PRO SER VAL THR ALA SEQRES 2 B 225 MET ARG VAL ILE ALA SER VAL ASN ALA ASP PHE ALA ARG SEQRES 3 B 225 GLU LEU LYS LEU PRO PRO HIS ILE ARG SER LEU GLY LEU SEQRES 4 B 225 ILE SER ALA ASP SER ASP ASP VAL THR TYR ILE ALA ALA SEQRES 5 B 225 ASP GLU ALA THR LYS GLN ALA MET VAL GLU VAL VAL TYR SEQRES 6 B 225 GLY ARG SER LEU TYR ALA GLY ALA ALA HIS GLY PRO SER SEQRES 7 B 225 PRO THR ALA GLY GLU VAL LEU ILE MET LEU GLY GLY PRO SEQRES 8 B 225 ASN PRO ALA GLU VAL ARG ALA GLY LEU ASP ALA MET ILE SEQRES 9 B 225 ALA HIS ILE GLU ASN GLY ALA ALA PHE GLN TRP ALA ASN SEQRES 10 B 225 ASP ALA GLN ASP THR ALA PHE LEU ALA HIS VAL VAL SER SEQRES 11 B 225 ARG THR GLY SER TYR LEU SER SER THR ALA GLY ILE THR SEQRES 12 B 225 LEU GLY ASP PRO MET ALA TYR LEU VAL ALA PRO PRO LEU SEQRES 13 B 225 GLU ALA THR TYR GLY ILE ASP ALA ALA LEU LYS SER ALA SEQRES 14 B 225 ASP VAL GLN LEU ALA THR TYR VAL PRO PRO PRO SER GLU SEQRES 15 B 225 THR ASN TYR SER ALA ALA PHE LEU THR GLY SER GLN ALA SEQRES 16 B 225 ALA CYS LYS ALA ALA CYS ASN ALA PHE THR ASP ALA VAL SEQRES 17 B 225 LEU GLU ILE ALA ARG ASN PRO ILE GLN ARG ALA HIS HIS SEQRES 18 B 225 HIS HIS HIS HIS HET BME A 226 4 HET ZN A 901 1 HET ZN A 902 1 HET ZN A 903 1 HET ZN B 904 1 HET ZN B 905 1 HETNAM BME BETA-MERCAPTOETHANOL HETNAM ZN ZINC ION FORMUL 3 BME C2 H6 O S FORMUL 4 ZN 5(ZN 2+) FORMUL 9 HOH *13(H2 O) HELIX 1 1 ASN A 21 LEU A 28 1 8 HELIX 2 2 ASP A 45 THR A 56 1 12 HELIX 3 3 PRO A 93 ASN A 109 1 17 HELIX 4 4 PRO A 154 LYS A 167 1 14 HELIX 5 5 GLN A 194 ASN A 214 1 21 HELIX 6 6 ASN B 21 LEU B 28 1 8 HELIX 7 7 SER B 44 ALA B 59 1 16 HELIX 8 8 ASN B 92 ASN B 109 1 18 HELIX 9 9 PRO B 154 ALA B 169 1 16 HELIX 10 10 SER B 193 ASN B 214 1 22 SHEET 1 A 4 VAL A 11 ILE A 17 0 SHEET 2 A 4 SER A 36 ALA A 42 -1 O LEU A 39 N ARG A 15 SHEET 3 A 4 ILE A 86 GLY A 90 -1 O GLY A 90 N SER A 36 SHEET 4 A 4 GLU A 62 VAL A 63 -1 N GLU A 62 O GLY A 89 SHEET 1 B 5 GLN A 114 TRP A 115 0 SHEET 2 B 5 ALA A 123 VAL A 129 -1 O PHE A 124 N GLN A 114 SHEET 3 B 5 MET A 148 ALA A 153 -1 O MET A 148 N VAL A 129 SHEET 4 B 5 SER A 186 THR A 191 -1 O ALA A 188 N LEU A 151 SHEET 5 B 5 GLN A 172 LEU A 173 -1 N GLN A 172 O THR A 191 SHEET 1 C 4 ALA B 13 ILE B 17 0 SHEET 2 C 4 SER B 36 ALA B 42 -1 O LEU B 37 N ILE B 17 SHEET 3 C 4 VAL B 84 GLY B 90 -1 O LEU B 88 N GLY B 38 SHEET 4 C 4 GLU B 62 ARG B 67 -1 N TYR B 65 O MET B 87 SHEET 1 D 2 GLN B 114 TRP B 115 0 SHEET 2 D 2 ALA B 123 PHE B 124 -1 O PHE B 124 N GLN B 114 SHEET 1 E 4 ALA B 126 VAL B 129 0 SHEET 2 E 4 MET B 148 LEU B 151 -1 O MET B 148 N VAL B 129 SHEET 3 E 4 ALA B 188 GLY B 192 -1 O ALA B 188 N LEU B 151 SHEET 4 E 4 VAL B 171 LEU B 173 -1 N GLN B 172 O THR B 191 LINK ND1 HIS A 127 ZN ZN A 901 1555 1555 2.32 LINK OE1 GLU A 157 ZN ZN A 903 1555 1555 2.26 LINK O1 BME A 226 ZN ZN A 901 1555 1555 2.51 LINK OE2 GLU B 157 ZN ZN B 905 1555 1555 2.43 SITE 1 AC1 3 ALA A 126 CYS A 201 ZN A 901 SITE 1 AC2 3 ALA A 126 HIS A 127 BME A 226 SITE 1 AC3 1 ARG A 97 SITE 1 AC4 1 GLU A 157 SITE 1 AC5 2 LEU B 156 GLU B 157 CRYST1 67.415 67.415 79.604 90.00 90.00 120.00 P 3 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 0.014833 0.008564 0.000000 0.00000 SCALE2 0.000000 0.017128 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012562 0.00000