HEADER HYDROLASE, BIOSYNTHETIC PROTEIN 08-MAY-08 3D2O TITLE CRYSTAL STRUCTURE OF MANGANESE-METALLATED GTP CYCLOHYDROLASE TYPE IB COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0343 PROTEIN NGO0387; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.5.4.16; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 485; SOURCE 4 ATCC: 700825; SOURCE 5 GENE: NGO0387; 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; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSAB-8-142 KEYWDS BIMODULAR TUNNEL FOLD, TUNNELING FOLD, FOLATE BIOSYNTHESIS, GTP KEYWDS 2 CYCLOHYDROLASE, METALLOENZYME, MANGANESE, HYDROLASE, BIOSYNTHETIC KEYWDS 3 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.SWAIRJO REVDAT 5 30-AUG-23 3D2O 1 REMARK LINK REVDAT 4 24-JUL-19 3D2O 1 REMARK REVDAT 3 25-OCT-17 3D2O 1 REMARK REVDAT 2 10-NOV-09 3D2O 1 JRNL REVDAT 1 12-MAY-09 3D2O 0 JRNL AUTH B.SANKARAN,S.A.BONNETT,K.SHAH,S.GABRIEL,R.REDDY,P.SCHIMMEL, JRNL AUTH 2 D.A.RODIONOV,V.DE CRECY-LAGARD,J.D.HELMANN,D.IWATA-REUYL, JRNL AUTH 3 M.A.SWAIRJO JRNL TITL ZINC-INDEPENDENT FOLATE BIOSYNTHESIS: GENETIC, BIOCHEMICAL, JRNL TITL 2 AND STRUCTURAL INVESTIGATIONS REVEAL NEW METAL DEPENDENCE JRNL TITL 3 FOR GTP CYCLOHYDROLASE IB JRNL REF J.BACTERIOL. V. 191 6936 2009 JRNL REFN ISSN 0021-9193 JRNL PMID 19767425 JRNL DOI 10.1128/JB.00287-09 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.EL YACOUBI,S.BONNETT,J.A.ANDERSON,M.A.SWAIRJO, REMARK 1 AUTH 2 D.IWATA-REUYL,V.DE CRECY-LAGARD REMARK 1 TITL DISCOVERY OF A NEW PROKARYOTIC TYPE I GTP CYCLOHYDROLASE REMARK 1 TITL 2 FAMILY REMARK 1 REF J.BIOL.CHEM. V. 281 37586 2006 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 17032654 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 33647 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1710 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2251 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 127 REMARK 3 BIN FREE R VALUE : 0.3110 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3829 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 261 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.07000 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): 0.197 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.475 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3905 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5285 ; 1.754 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 485 ; 6.962 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;37.185 ;23.964 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 695 ;16.604 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;22.331 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 609 ; 0.122 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2901 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1702 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2678 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 252 ; 0.158 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.181 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 126 ; 0.240 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 21 ; 0.167 ; 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): 2522 ; 1.420 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3954 ; 2.184 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1570 ; 3.290 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1331 ; 4.451 ; 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): 4092 ; 2.302 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 272 ; 8.842 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3832 ; 4.391 ; 3.000 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 : NULL 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 3D2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.97607 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL (SI111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33675 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42800 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: CNS REMARK 200 STARTING MODEL: PDB ENTRY 3D1T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: (PEG 6000, 10-16%), LICL (1-1.4 M), REMARK 280 TRIS (50 MM, PH 9.0) AND TRIS-CL (50 MM, PH 7.0). ENZYM SAMPLE REMARK 280 PREPARED AT 10 MG/ML IN 50 MM TRIS-HCL, 50 MM KCL, 1 MM DTT, PH REMARK 280 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.97350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.97350 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 46.11250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.11250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.97350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.11250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.21000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.97350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.11250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.21000 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.4 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 100.42000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 315 LIES ON A SPECIAL POSITION. 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 ASN A 2 REMARK 465 ALA A 3 REMARK 465 ILE A 4 REMARK 465 ALA A 5 REMARK 465 ASP A 6 REMARK 465 VAL A 7 REMARK 465 GLN A 8 REMARK 465 SER A 9 REMARK 465 SER A 10 REMARK 465 ARG A 11 REMARK 465 ASP A 12 REMARK 465 LEU A 13 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 ALA B 3 REMARK 465 ILE B 4 REMARK 465 ALA B 5 REMARK 465 ASP B 6 REMARK 465 VAL B 7 REMARK 465 GLN B 8 REMARK 465 SER B 9 REMARK 465 SER B 10 REMARK 465 ARG B 11 REMARK 465 ASP B 12 REMARK 465 LEU B 13 REMARK 465 ARG B 14 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 90 CA - CB - CG ANGL. DEV. = -16.5 DEGREES REMARK 500 ARG B 27 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 27 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 LEU B 90 CA - CB - CG ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG B 162 NE - CZ - NH2 ANGL. DEV. = -3.3 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 LEU A 16 119.37 80.99 REMARK 500 LEU B 16 113.28 88.91 REMARK 500 THR B 58 -165.48 -100.94 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 ARG A 14 ASN A 15 -145.36 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 MN A 258 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 147 SG REMARK 620 2 HIS A 159 NE2 101.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 258 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 147 SG REMARK 620 2 HIS B 159 NE2 106.5 REMARK 620 3 AZI B 261 N1 113.6 116.0 REMARK 620 4 HOH B 406 O 89.5 162.3 48.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: NULL REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: NULL REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: NULL REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 261 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 258 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LI B 259 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZI B 261 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D1T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ZINC-METALLATED GTP CYCLOHYDROLASE TYPE IB DBREF 3D2O A 1 257 UNP Q5F9K6 Y387_NEIG1 1 257 DBREF 3D2O B 1 257 UNP Q5F9K6 Y387_NEIG1 1 257 SEQRES 1 A 257 MET ASN ALA ILE ALA ASP VAL GLN SER SER ARG ASP LEU SEQRES 2 A 257 ARG ASN LEU PRO ILE ASN GLN VAL GLY ILE LYS ASP LEU SEQRES 3 A 257 ARG PHE PRO ILE THR LEU LYS THR ALA GLU GLY THR GLN SEQRES 4 A 257 SER THR VAL ALA ARG LEU THR MET THR VAL TYR LEU PRO SEQRES 5 A 257 ALA GLU GLN LYS GLY THR HIS MET SER ARG PHE VAL ALA SEQRES 6 A 257 LEU MET GLU GLN HIS THR GLU VAL LEU ASP PHE ALA GLN SEQRES 7 A 257 LEU HIS ARG LEU THR ALA GLU MET VAL ALA LEU LEU ASP SEQRES 8 A 257 SER ARG ALA GLY LYS ILE SER VAL SER PHE PRO PHE PHE SEQRES 9 A 257 ARG LYS LYS THR ALA PRO VAL SER GLY ILE ARG SER LEU SEQRES 10 A 257 LEU ASP TYR ASP VAL SER LEU THR GLY GLU MET LYS ASP SEQRES 11 A 257 GLY ALA TYR GLY HIS SER MET LYS VAL MET ILE PRO VAL SEQRES 12 A 257 THR SER LEU CYS PRO CYS SER LYS GLU ILE SER GLN TYR SEQRES 13 A 257 GLY ALA HIS ASN GLN ARG SER HIS VAL THR VAL SER LEU SEQRES 14 A 257 THR SER ASP ALA GLU VAL GLY ILE GLU GLU VAL ILE ASP SEQRES 15 A 257 TYR VAL GLU THR GLN ALA SER CYS GLN LEU TYR GLY LEU SEQRES 16 A 257 LEU LYS ARG PRO ASP GLU LYS TYR VAL THR GLU LYS ALA SEQRES 17 A 257 TYR GLU ASN PRO LYS PHE VAL GLU ASP MET VAL ARG ASP SEQRES 18 A 257 VAL ALA THR SER LEU ILE ALA ASP LYS ARG ILE LYS SER SEQRES 19 A 257 PHE VAL VAL GLU SER GLU ASN PHE GLU SER ILE HIS ASN SEQRES 20 A 257 HIS SER ALA TYR ALA TYR ILE ALA TYR PRO SEQRES 1 B 257 MET ASN ALA ILE ALA ASP VAL GLN SER SER ARG ASP LEU SEQRES 2 B 257 ARG ASN LEU PRO ILE ASN GLN VAL GLY ILE LYS ASP LEU SEQRES 3 B 257 ARG PHE PRO ILE THR LEU LYS THR ALA GLU GLY THR GLN SEQRES 4 B 257 SER THR VAL ALA ARG LEU THR MET THR VAL TYR LEU PRO SEQRES 5 B 257 ALA GLU GLN LYS GLY THR HIS MET SER ARG PHE VAL ALA SEQRES 6 B 257 LEU MET GLU GLN HIS THR GLU VAL LEU ASP PHE ALA GLN SEQRES 7 B 257 LEU HIS ARG LEU THR ALA GLU MET VAL ALA LEU LEU ASP SEQRES 8 B 257 SER ARG ALA GLY LYS ILE SER VAL SER PHE PRO PHE PHE SEQRES 9 B 257 ARG LYS LYS THR ALA PRO VAL SER GLY ILE ARG SER LEU SEQRES 10 B 257 LEU ASP TYR ASP VAL SER LEU THR GLY GLU MET LYS ASP SEQRES 11 B 257 GLY ALA TYR GLY HIS SER MET LYS VAL MET ILE PRO VAL SEQRES 12 B 257 THR SER LEU CYS PRO CYS SER LYS GLU ILE SER GLN TYR SEQRES 13 B 257 GLY ALA HIS ASN GLN ARG SER HIS VAL THR VAL SER LEU SEQRES 14 B 257 THR SER ASP ALA GLU VAL GLY ILE GLU GLU VAL ILE ASP SEQRES 15 B 257 TYR VAL GLU THR GLN ALA SER CYS GLN LEU TYR GLY LEU SEQRES 16 B 257 LEU LYS ARG PRO ASP GLU LYS TYR VAL THR GLU LYS ALA SEQRES 17 B 257 TYR GLU ASN PRO LYS PHE VAL GLU ASP MET VAL ARG ASP SEQRES 18 B 257 VAL ALA THR SER LEU ILE ALA ASP LYS ARG ILE LYS SER SEQRES 19 B 257 PHE VAL VAL GLU SER GLU ASN PHE GLU SER ILE HIS ASN SEQRES 20 B 257 HIS SER ALA TYR ALA TYR ILE ALA TYR PRO HET MN A 258 1 HET MN B 258 1 HET LI B 259 1 HET CL B 260 1 HET AZI B 261 3 HETNAM MN MANGANESE (II) ION HETNAM LI LITHIUM ION HETNAM CL CHLORIDE ION HETNAM AZI AZIDE ION FORMUL 3 MN 2(MN 2+) FORMUL 5 LI LI 1+ FORMUL 6 CL CL 1- FORMUL 7 AZI N3 1- FORMUL 8 HOH *261(H2 O) HELIX 1 1 MET A 60 HIS A 70 1 11 HELIX 2 2 ASP A 75 LEU A 90 1 16 HELIX 3 3 CYS A 147 SER A 154 1 8 HELIX 4 4 GLY A 176 THR A 186 1 11 HELIX 5 5 LYS A 197 ASN A 211 1 15 HELIX 6 6 PHE A 214 ASP A 229 1 16 HELIX 7 7 MET B 60 HIS B 70 1 11 HELIX 8 8 ASP B 75 LEU B 90 1 16 HELIX 9 9 CYS B 147 SER B 154 1 8 HELIX 10 10 GLY B 176 ALA B 188 1 13 HELIX 11 11 LYS B 197 ASN B 211 1 15 HELIX 12 12 PHE B 214 ALA B 228 1 15 SHEET 1 A11 CYS A 190 GLN A 191 0 SHEET 2 A11 ALA A 132 LEU A 146 -1 N THR A 144 O CYS A 190 SHEET 3 A11 ARG A 115 LYS A 129 -1 N ASP A 121 O MET A 140 SHEET 4 A11 ALA A 94 THR A 108 -1 N PHE A 103 O TYR A 120 SHEET 5 A11 GLY A 37 LEU A 51 -1 N THR A 46 O SER A 98 SHEET 6 A11 ILE A 18 THR A 34 -1 N LEU A 32 O GLN A 39 SHEET 7 A11 SER B 249 TYR B 256 -1 O TYR B 251 N GLY A 22 SHEET 8 A11 ILE B 232 ASN B 241 -1 N PHE B 235 O TYR B 256 SHEET 9 A11 ASN B 160 SER B 171 -1 N HIS B 164 O GLU B 240 SHEET 10 A11 ALA B 132 LEU B 146 -1 N ILE B 141 O VAL B 165 SHEET 11 A11 CYS B 190 GLN B 191 -1 O CYS B 190 N THR B 144 SHEET 1 B11 CYS A 190 GLN A 191 0 SHEET 2 B11 ALA A 132 LEU A 146 -1 N THR A 144 O CYS A 190 SHEET 3 B11 ASN A 160 SER A 171 -1 O VAL A 165 N ILE A 141 SHEET 4 B11 ILE A 232 ASN A 241 -1 O GLU A 238 N THR A 166 SHEET 5 B11 SER A 249 TYR A 256 -1 O TYR A 256 N PHE A 235 SHEET 6 B11 ILE B 18 THR B 34 -1 O GLY B 22 N TYR A 251 SHEET 7 B11 GLY B 37 LEU B 51 -1 O GLN B 39 N LEU B 32 SHEET 8 B11 ALA B 94 THR B 108 -1 O ALA B 94 N TYR B 50 SHEET 9 B11 ARG B 115 LYS B 129 -1 O SER B 116 N LYS B 107 SHEET 10 B11 ALA B 132 LEU B 146 -1 O MET B 140 N ASP B 121 SHEET 11 B11 CYS B 190 GLN B 191 -1 O CYS B 190 N THR B 144 LINK SG CYS A 147 MN MN A 258 1555 1555 2.43 LINK NE2 HIS A 159 MN MN A 258 1555 1555 2.32 LINK SG CYS B 147 MN MN B 258 1555 1555 2.47 LINK NE2 HIS B 159 MN MN B 258 1555 1555 2.13 LINK MN MN B 258 N1 AZI B 261 1555 1555 2.69 LINK MN MN B 258 O HOH B 406 1555 1555 2.73 CISPEP 1 TYR A 256 PRO A 257 0 2.27 CISPEP 2 TYR B 256 PRO B 257 0 1.22 SITE 1 AC1 3 CYS B 147 HIS B 159 GLU B 201 SITE 1 AC2 3 CYS A 147 HIS A 159 GLU A 201 SITE 1 AC3 2 GLU B 243 HIS B 246 SITE 1 AC4 3 CYS A 147 HIS A 159 GLU A 201 SITE 1 AC5 5 CYS B 147 HIS B 159 GLU B 201 AZI B 261 SITE 2 AC5 5 HOH B 406 SITE 1 AC6 1 ILE B 232 SITE 1 AC7 4 GLU B 243 HIS B 246 MN B 258 HOH B 406 CRYST1 92.225 100.420 113.947 90.00 90.00 90.00 C 2 2 21 16 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 0.010843 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008776 0.00000