HEADER PHOSPHOTRANSFERASE 19-MAY-98 2GPR TITLE GLUCOSE PERMEASE IIA FROM MYCOPLASMA CAPRICOLUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-PERMEASE IIA COMPONENT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DOMAIN IIA; COMPND 5 EC: 2.7.1.69; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA CAPRICOLUM; SOURCE 3 ORGANISM_TAXID: 2095; SOURCE 4 STRAIN: KID; SOURCE 5 ATCC: ATCC 27343; SOURCE 6 COLLECTION: ATCC 27343; SOURCE 7 CELLULAR_LOCATION: CYTOPLASM; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOTRANSFERASE, GLUCOSE PERMEASE, ENZYME IIA, MYCOPLASMA EXPDTA X-RAY DIFFRACTION AUTHOR K.HUANG,O.HERZBERG REVDAT 5 29-MAY-24 2GPR 1 REMARK REVDAT 4 09-AUG-23 2GPR 1 REMARK REVDAT 3 24-FEB-09 2GPR 1 VERSN REVDAT 2 01-APR-03 2GPR 1 JRNL REVDAT 1 12-AUG-98 2GPR 0 JRNL AUTH K.HUANG,G.KAPADIA,P.P.ZHU,A.PETERKOFSKY,O.HERZBERG JRNL TITL A PROMISCUOUS BINDING SURFACE: CRYSTAL STRUCTURE OF THE IIA JRNL TITL 2 DOMAIN OF THE GLUCOSE-SPECIFIC PERMEASE FROM MYCOPLASMA JRNL TITL 3 CAPRICOLUM. JRNL REF STRUCTURE V. 6 697 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9705652 JRNL DOI 10.1016/S0969-2126(98)00072-0 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5 REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 4296 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1167 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 62 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.018 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 2.280 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 20.200; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.020 ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : 0.019 ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.600 ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : 0.036 ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : BABINET SCALING REMARK 3 KSOL : 0.60 REMARK 3 BSOL : 134.2 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GPR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-95 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RUH2R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : XENGEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4952 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 28.3000 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1GPR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 20-30% REMARK 280 PEG 3000, 0.3MM ZNCL2, 100MM TRIS-HCL BUFFER, PH 7.5. 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 20.16500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.94500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.94500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.82500 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: MONOMERIC 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 TRP A 7 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 7 CZ3 CH2 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 OE1 GLU A 105 O HOH A 167 2.00 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 OD1 ASP A 87 NZ LYS A 159 3655 1.95 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 A 32 CD GLU A 32 OE2 0.079 REMARK 500 GLU A 36 CD GLU A 36 OE1 0.073 REMARK 500 GLU A 97 CD GLU A 97 OE2 0.086 REMARK 500 GLU A 142 CB GLU A 142 CG 0.119 REMARK 500 GLU A 142 CG GLU A 142 CD 0.114 REMARK 500 GLU A 148 CD GLU A 148 OE2 0.076 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 27 CB - CG - OD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 31 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 31 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ASP A 51 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP A 87 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 103 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 110 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 GLU A 142 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 ASP A 153 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 153 CB - CG - OD2 ANGL. DEV. = 5.7 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 ASN A 10 141.58 -179.20 REMARK 500 ASP A 31 115.18 -167.73 REMARK 500 ASP A 87 -3.73 62.10 REMARK 500 ASP A 103 -6.60 75.55 REMARK 500 ASN A 136 -82.05 -128.58 REMARK 500 LYS A 139 30.37 -44.04 REMARK 500 REMARK 500 REMARK: NULL DBREF 2GPR A 6 159 UNP P45618 PTGA_MYCCA 1 154 SEQRES 1 A 154 MET TRP PHE PHE ASN LYS ASN LEU LYS VAL LEU ALA PRO SEQRES 2 A 154 CYS ASP GLY THR ILE ILE THR LEU ASP GLU VAL GLU ASP SEQRES 3 A 154 GLU VAL PHE LYS GLU ARG MET LEU GLY ASP GLY PHE ALA SEQRES 4 A 154 ILE ASN PRO LYS SER ASN ASP PHE HIS ALA PRO VAL SER SEQRES 5 A 154 GLY LYS LEU VAL THR ALA PHE PRO THR LYS HIS ALA PHE SEQRES 6 A 154 GLY ILE GLN THR LYS SER GLY VAL GLU ILE LEU LEU HIS SEQRES 7 A 154 ILE GLY LEU ASP THR VAL SER LEU ASP GLY ASN GLY PHE SEQRES 8 A 154 GLU SER PHE VAL THR GLN ASP GLN GLU VAL ASN ALA GLY SEQRES 9 A 154 ASP LYS LEU VAL THR VAL ASP LEU LYS SER VAL ALA LYS SEQRES 10 A 154 LYS VAL PRO SER ILE LYS SER PRO ILE ILE PHE THR ASN SEQRES 11 A 154 ASN GLY GLY LYS THR LEU GLU ILE VAL LYS MET GLY GLU SEQRES 12 A 154 VAL LYS GLN GLY ASP VAL VAL ALA ILE LEU LYS FORMUL 2 HOH *62(H2 O) HELIX 1 1 LEU A 26 GLU A 28 5 3 HELIX 2 2 GLU A 32 LYS A 35 1 4 HELIX 3 3 THR A 88 LEU A 91 5 4 HELIX 4 4 LEU A 117 LYS A 123 1 7 SHEET 1 A 7 GLY A 147 VAL A 149 0 SHEET 2 A 7 GLY A 21 ILE A 24 -1 N ILE A 23 O GLY A 147 SHEET 3 A 7 ASP A 41 PRO A 47 -1 N ASN A 46 O THR A 22 SHEET 4 A 7 SER A 129 ASN A 135 -1 N PHE A 133 O ASP A 41 SHEET 5 A 7 GLU A 79 HIS A 83 -1 N HIS A 83 O PRO A 130 SHEET 6 A 7 ALA A 69 GLN A 73 -1 N ILE A 72 O ILE A 80 SHEET 7 A 7 LYS A 59 THR A 62 -1 N THR A 62 O GLY A 71 SHEET 1 B 3 PHE A 96 SER A 98 0 SHEET 2 B 3 LYS A 111 VAL A 115 -1 N THR A 114 O GLU A 97 SHEET 3 B 3 ASP A 51 HIS A 53 -1 N PHE A 52 O LEU A 112 SHEET 1 C 2 LEU A 13 LEU A 16 0 SHEET 2 C 2 VAL A 154 LEU A 158 -1 N LEU A 158 O LEU A 13 CRYST1 40.330 47.650 71.890 90.00 90.00 90.00 P 21 21 21 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 0.024795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020986 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013910 0.00000